VprBP directs epigenetic gene silencing through histone H2A phosphorylation in colon cancer

Histone modification is aberrantly regulated in cancer and generates an unbalanced state of gene transcription. VprBP, a recently identified kinase, phosphorylates histone H2A on threonine 120 (T120) and is involved in oncogenic transcriptional dysregulation; however, its specific role in colon cancer is undefined. Here, we show that VprBP is overexpressed in colon cancer and directly contributes to epigenetic gene silencing and cancer pathogenesis. Mechanistically, the observed function of VprBP is mediated through H2AT120 phosphorylation (H2AT120p)‐driven transcriptional repression of growth regulatory genes, resulting in a significantly higher proliferative capacity of colon cancer cells. Our preclinical studies using organoid and xenograft models demonstrate that treatment with the VprBP inhibitor B32B3 impairs colonic tumor growth by blocking H2AT120p and reactivating a transcriptional program resembling that of normal cells. Collectively, our work describes VprBP as a master kinase contributing to the development and progression of colon cancer, making it a new molecular target for novel therapeutic strategies.

Human colorectal cancer-on-chip model to study the microenvironmental influence on early metastatic spread

Colorectal cancer (CRC) progression is a complex process that is not well understood. We describe an in vitro organ-on-chip model that emulates in vivo tissue structure and the tumor microenvironment (TME) to better understand intravasation, an early step in metastasis. The CRC-on-chip incorporates fluid flow and peristalsis-like cyclic stretching and consists of endothelial and epithelial compartments, separated by a porous membrane. On-chip imaging and effluent analyses are used to interrogate CRC progression and the resulting cellular heterogeneity. Mass spectrometry-based metabolite profiles are indicative of a CRC disease state. Tumor cells intravasate from the epithelial channel to the endothelial channel, revealing differences in invasion between aggressive and non-aggressive tumor cells. Tuning the TME by peristalsis-like mechanical forces, the epithelial:endothelial interface, and the addition of fibroblasts influences the invasive capabilities of tumor cells. The CRC-on-chip is a tunable human-relevant model system and a valuable tool to study early invasive events in cancer.

Comparison of Cell and Organoid-Level Analysis of Patient-Derived 3D Organoids to Evaluate Tumor Cell Growth Dynamics and Drug Response

3D cell culture models have been developed to better mimic the physiological environments that exist in human diseases. As such, these models are advantageous over traditional 2D cultures for screening drug compounds. However, the practicalities of transitioning from 2D to 3D drug treatment studies pose challenges with respect to analysis methods. Patient-derived tumor organoids (PDTOs) possess unique features given their heterogeneity in size, shape, and growth patterns. A detailed assessment of the length scale at which PDTOs should be evaluated (i.e., individual cell or organoid-level analysis) has not been done to our knowledge. Therefore, using dynamic confocal live cell imaging and data analysis methods we examined tumor cell growth rates and drug response behaviors in colorectal cancer (CRC) PDTOs. High-resolution imaging of H2B-GFP-labeled organoids with DRAQ7 vital dye permitted tracking of cellular changes, such as cell birth and death events, in individual organoids. From these same images, we measured morphological features of the 3D objects, including volume, sphericity, and ellipticity. Sphericity and ellipticity were used to evaluate intra- and interpatient tumor organoid heterogeneity. We found a strong correlation between organoid live cell number and volume. Linear growth rate calculations based on volume or live cell counts were used to determine differential responses to therapeutic interventions. We showed that this approach can detect different types of drug effects (cytotoxic vs cytostatic) in PDTO cultures. Overall, our imaging-based quantification workflow results in multiple parameters that can provide patient- and drug-specific information for screening applications.

Abstract 5786: Histopathology of patient derived organoids for the quantitative analysis of response to microenvironmental perturbations

Patient derived organoids are becoming a popular 3D in vitro model that more accurately recapitulate in vivo conditions compared to standard 2D culture systems. Organoids consist of epithelial cells and lack stroma and mesenchyme, allowing cells of interest to be studied as an isolated system. However, the tunability of the organoid model also permits the re-addition of microenvironmental factors, i.e. cancer associated fibroblasts (CAFs), resulting in a wide range of experimental capabilities. Organoids are easily scalable, making them more efficient and cost-effective than traditional animal models. Despite the popularity of animal models for pre-clinical drug testing, there still remain issues with translating results from animal testing to patient outcomes; even patient-derived xenograph models experience non-physiological mouse-human interactions. Therefore, studying the impact of microenvironmental perturbations, such as the presence of CAFs, or nutrient and drug gradients, on organoids may reduce translational error. Using our biorepository of patient derived colon cancer (primary and liver metastases) organoids, we can observe changes in tumor architecture and cell growth or death, allowing us to more accurately assess the efficacy of drug therapies and observe how interpatient heterogeneity impacts their efficacy. Here we focus on the histopathology of different patient derived organoids to quantitatively study cell growth or death under drug treatments (+/- CAFs) which could ultimately become a standard procedure for drug screening.

Here we investigate the effects of CAF co-culture in patient derived organoids in response to standard chemotherapies such as Irinotecan and Oxaliplatin. Following treatment, the organoids are paraffin fixed to retain their structural integrity, then sectioned. The samples are stained with H&E to show the tumor architecture, and immunofluorescent antibodies (IF) to identify cells that are proliferating (Ki67) or apoptotic (TUNEL). As a result, we are able to investigate how tumor microenvironmental factors affect the tumor architecture of an individual patient tumor. We also examine the cytotoxic or cytostatic effects of standard chemotherapies by quantitating the number of proliferative and apoptotic cells, as well as their location within the tumor, in response to the presence of both CAFs and therapy.

Ultimately, we envision the method outlined here will further personalize medicine by allowing physicians to more rapidly assess an individual patient’s response to therapy and adjust treatment accordingly. Additionally, this method could prove to be a more inexpensive and faster means of screening new drug compounds. By creating a system that more closely recapitulates patient outcomes, we hope to move therapies towards faster approval while still retaining results representative of in vivo outcomes.

Citation Format: Sarah J. Choung, Erin Spiller, Roy Lau, Shannon Mumenthaler. Histopathology of patient derived organoids for the quantitative analysis of response to microenvironmental perturbations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5786. doi:10.1158/1538-7445.AM2017-5786

Abstract A18: High-content 3D image analysis of patient-derived organoids

Organoids are an emerging model system that more closely recapitulates the in vivo environment compared to traditional monolayer systems. Using patient-derived samples grown in a 3D matrix, we hope to advance personalized medicine by providing more patient-specific treatment plans. We have begun building a patient-derived organoid library from primary colon cancer tumors and metastases. Once cells are isolated and seeded into a Basement Membrane Extract (BME) matrix we analyze features on a high content imaging platform, the Operetta (Perkin Elmer). Using the Operetta we are able to obtain quantitative phenotypic data that includes the number, size, and morphology of organoids. In addition, we can capture the dynamics of organoid formation, growth, and death by tracking the same organoids over time using live-cell imaging.

More specifically, for each organoid, we capture z-stack images at various heights, and using the Harmony software, we perform quantitative analysis on the maximum projection of the complied images. Using a building block approach, we created a workflow that first relied on identifying regions of interest (ROI), which correspond to organoids. In each ROI we then obtained information such as geometric center, length and width measurements, and texture features. We used this information to determine inter-patient heterogeneity, as well as differences across samples isolated from the primary location (i.e. colon) versus metastatic sites (i.e. liver). After culturing patient-derived organoids for several weeks in laboratory conditions, we perturbed various aspects of the tumor microenvironment (e.g. drug and oxygen levels) and subsequently tracked changes in organoid number, size, and morphology over time. This workflow represents a unique method for image-based quantitative phenotypic analysis of organoids under varying environmental conditions.

Citation Format: Erin Spiller, Roy Lau, Sarah Choung, Shannon M. Mumenthaler. High-content 3D image analysis of patient-derived organoids. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A18.

A silicon-based, sequential coat-and-etch process to fabricate nearly perfect substrate surfaces

For many thin-film applications substrate imperfections such as particles, pits, scratches, and general roughness, can nucleate film defects which can severely detract from the coating's performance. Previously we developed a coat-and-etch process, termed the ion beam thin film planarization process, to planarize substrate particles up to approximately 70 nm in diameter. The process relied on normal incidence etching; however, such a process induces defects nucleated by substrate pits to grow much larger. We have since developed a coat-and-etch process to planarize approximately 70 nm deep by 70 nm wide substrate pits; it relies on etching at an off-normal incidence angle, i.e., an angle of approximately 470 degrees from the substrate normal. However, a disadvantage of this pit smoothing process is that it induces defects nucleated by substrate particles to grow larger. Combining elements from both processes we have been able to develop a silicon-based, coat-and-etch process to successfully planarize approximately 70 nm substrate particles and pits simultaneously to at or below 1 nm in height; this value is important for applications such as extreme ultraviolet lithography (EUVL) masks. The coat-and-etch process has an added ability to significantly reduce high-spatial frequency roughness, rendering a nearly perfect substrate surface.

Diffraction-limited large x-ray optics

It is shown that the technologies required to produce large normal-incidence multilayer x-ray mirrors with diffraction-limited resolution are now available. Applications of these mirrors in x-ray astronomy and x-ray lithography are discussed.

Refractive index of amorphous carbon near its K-edge

The refractive index of the amorphous carbon layers inside multilayer soft x-ray mirrors is derived in the lambda = 42-58-A wavelength range by measuring the shift in the Bragg angle caused by refraction. Reflectivity curves are measured with a reflectometer behind a zone plate monochromator at the National Synchrotron Light Source. The monochromator consists only of a freestanding zone plate of gold and an exit slit and is free of any of the contamination problems often found in monochromators that contain mirrors.

Large area coatings with uniform thickness fabricated in a small vacuum chamber

Evaporative atom reflections from chamber walls are used to enhance direct line deposition. Interfacial surface roughness is reduced by depositing at near normal incidence. Film thickness depends on the mass of the evaporant and the chamber geometry.

Fabrication and testing of large area multilayer coated x-ray optics

We discuss the procedures developed for the production and testing of multilayer x-ray mirrors on large figured optical surfaces. Methods which are generally useful for characterizing the performance of such optics are presented, as well as specific results from the production of a 25-cm diam Ritchey-Chretien telescope for a wavelength of lambda = 63.5 A. The latter is a two-mirror system, which places additional stringent requirements upon the accuracy and quality of the coatings.

Graded-index AR surfaces produced by ion implantation on plastic materials

The damage tracks of high energy ions in dielectric materials can be etched until overlapping conical etch pits are obtained. If the depth of the pits is >lambda/2, an effective graded-index layer with very low reflectivity is obtained. Broadband antireflection treatment achieving reflectivities of <10(-4) has been applied to plastics like Lexan and Mylar.

High resolution microchemical analysis using soft X-ray lithographic techniques

High resolution x-ray lithographic studies of cells from chick embryo hearts dried by the CO2 critical point method have been made with soft x-ray radiation of different wavelengths. A marked difference in the relief replica in polymethyl methacrylate (PMMA) resulting from the differential absorption by the dried cells of carbon K alpha radiation at 4.48 nm and broad band synchrotron radiation (SR) with lambda is greater than 1.5 nm demonstrates the potential usefulness of the technique in making high resolution (approximately or equal to 10 nm) chemical identification of the constitutents which make up the various parts of the cell.

Transmission microscropy of unmodified biological materials: comparative radiation dosages with electrons and ultrasoft x-ray photons

The minimum radiation dosage in a specimen consistent with transmission microscopy at resolution d and specimen thickness t is calculated for model specimens resembling biological materials in their natural state. The calculations cover 10(4)-10(7) eV electrons and 1.3-90 A photons in a number of microscopy modes. The results indicate that over a considerable part of the (t,d)-plane transmission microscopy on such specimens can be carried out at lower dosage with photons than with electrons. Estimates of the maximum resolutions obtainable with electrons and photons, consistent with structural survival of the specimen, are obtained, as are data on optimal operating conditions for microscopy with the two particles.

High-resolution soft x-ray microscopy

X-ray micrographs of biological materials have been obtained with a resolution better than 100 angstroms by using x-ray resist as the recording medium. A high-resolution scanning electron microscope with a short-focal-length final lens, operating in the "low-loss" mode, is used to make the smallest features in the x-ray replica visible.

Potential operating region for ultrasoft x-ray microscopy of biological materials

Calculations are presented which indicate an extensive suboptical region in the microscopy of biological materials in their natural state which is accessible to ultrasoft x-ray transmission microscopy. Throughout most of the region, radiation dosage levels to the specimen are lower than in electron microscopy.

Reflective multilayer coatings for the far uv region

Progress in the field of reflective multilayer coatings for the wavelength region between 50 A and 2000 A is reviewed. All the coatings contain absorbing materials, absorption losses are minimized by positioning strongly absorbing materials into the nodes of the standing wave inside the coating. Above lambda = 1200 A, ideal coatings with a reflectivity approaching 100% are theoretically possible; the theoretical predictions have been confirmed for coatings up to six layers at wavelengths around 2000 A. Below lambda = 1000 A, no absorption-free material is available that can be used as a spacer layer to cover the antinodes of the standing wave field. This limits the theoretically obtainable reflectivity. However, even at the shortest wavelength a reflectivity of 30% is still possible. Experimental results have been obtained for wavelengths between 100 A and 200 A for coatings up to nine layers. Discrepancies between experiment and theory can be explained as due to insufficient knowledge of the optical constants of the films used. Extensive future work on the optical constants of materials and their dependence on film thickness and deposition conditions is required for further improvement.

X-ray microscopy of biological objects with carbon kappa and with synchrotron radiation

X-ray micrographs of biological objects have been obtained with a resolution better than 1000 angstroms by using poly(methyl methacrylate) x-ray resist and carbon Kalpha or synchrotron radiation. Synchrotron radiation allows short exposure times; storage rings especially designed as radiation sources and improved x-ray resists would make exposure times under 1 second possible.

High resolution lenses for optical waveguides

A mode index lens and a lens formed by a spherical depression in the substrate of the waveguide have opposite aberrations and can be combined in an element with considerably reduced aberrations. Only small differences in the mode index are required for the optimum combination.

Interference filters for the ultraviolet and the surface plasmon of aluminum

It is shown that (Al-MgF(2))-interference filters of better performance than have been predicted and obtained previously are possible in the uv below 2500 A. Experimental results are given for conventional filters of first and higher order and for new filter designs that use multilayer structures for the two mirrors of the filter. All discrepancies between theoretical and experimental results are explained by a coupling of light into the surface plasmon of aluminum via a surface roughness of the MgF(2) films.

Broadening of short light pulses by many reflections from multilayer dielectric coatings

The broadening of short light pulses which are reflected from multilayer dielectric mirror coatings is calculated. The case when a pulse is reflected many times is treated in detail. The quarter-wave stack is the design for minimal pulse broadening. The broadening after many reflections is mainly due to the phase variations close to the edge of the reflection band of the coating. The shortest output pulses are obtained if only the center part of the reflection band of the mirror is used; an input pulse which contains only this part of the spectrum produces a much shorter output pulse than a delta-function input. Output pulses as short as 10(-13) sec are possible for typical mirror coatings and one-thousand reflections. The influence of errors in the fabrication of a coating on the calculated results is discussed.