@article{dutton_hinman_kim_attayek_maurer_sims_allbritton_2021, title={Hyperglycemia minimally alters primary self-renewing human colonic epithelial cells while TNF alpha-promotes severe intestinal epithelial dysfunction}, volume={13}, ISSN={["1757-9708"]}, DOI={10.1093/intbio/zyab008}, abstractNote={Abstract}, number={6}, journal={INTEGRATIVE BIOLOGY}, author={Dutton, Johanna S. and Hinman, Samuel S. and Kim, Raehyun and Attayek, Peter J. and Maurer, Mallory and Sims, Christopher S. and Allbritton, Nancy L.}, year={2021}, month={Jun}, pages={139–152} }
 @article{kim_attayek_wang_furtado_tamayo_sims_allbritton_2020, title={An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface}, volume={12}, ISSN={["1758-5090"]}, DOI={10.1088/1758-5090/ab446e}, abstractNote={An oxygen gradient formed along the length of colonic crypts supports stem-cell proliferation at the normoxic crypt base while supporting obligate anaerobe growth in the anoxic colonic lumen. Primary human colonic epithelial cells derived from human gastrointestinal stem cells were cultured within a device possessing materials of tailored oxygen permeability to produce an oxygen-depleted luminal (0.8% ± 0.1% O2) and oxygen-rich basal (11.1% ± 0.5% O2) compartment. This oxygen difference created a stable oxygen gradient across the colonic epithelial cells which remained viable and properly polarized. Facultative and obligate anaerobes Lactobacillus rhamnosus, Bifidobacterium adolescentis, and Clostridium difficile grew readily within the luminal compartment. When formed along the length of an in vitro crypt, the oxygen gradient facilitated cell compartmentalization within the crypt by enhancing confinement of the proliferative cells to the crypt base. This platform provides a simple system to create a physiological oxygen gradient across an intestinal mimic while simultaneously supporting anaerobe co-culture.}, number={1}, journal={BIOFABRICATION}, author={Kim, Raehyun and Attayek, Peter J. and Wang, Yuli and Furtado, Kathleen L. and Tamayo, Rita and Sims, Christopher E. and Allbritton, Nancy L.}, year={2020}, month={Jan} }
 @article{nowotarski_attayek_allbritton_2020, title={Automated platform for cell selection and separation based on four-dimensional motility and matrix degradation}, volume={145}, ISSN={["1364-5528"]}, DOI={10.1039/c9an02224d}, abstractNote={An automated platform to separate single cells based on matrix invasion was implemented on a microraft array to track inheritability of this complex phenotype.}, number={7}, journal={ANALYST}, author={Nowotarski, Hannah L. and Attayek, Peter J. and Allbritton, Nancy L.}, year={2020}, month={Apr}, pages={2731–2742} }
 @article{speer_gunasekara_wang_fallon_attayek_smith_sims_allbritton_2019, title={Molecular transport through primary human small intestinal monolayers by culture on a collagen scaffold with a gradient of chemical cross-linking}, volume={13}, ISSN={["1754-1611"]}, DOI={10.1186/s13036-019-0165-4}, abstractNote={The luminal surface of the small intestine is composed of a monolayer of cells overlying a lamina propria comprised of extracellular matrix (ECM) proteins. The ECM provides a porous substrate critical for nutrient exchange and cellular adhesion. The enterocytes within the epithelial monolayer possess proteins such as transporters, carriers, pumps and channels that participate in the movement of drugs, metabolites, ions and amino acids and whose function can be regulated or altered by the properties of the ECM. Here, we characterized expression and function of proteins involved in transport across the human small intestinal epithelium grown on two different culture platforms. One strategy employs a conventional scaffolding method comprised of a thin ECM film overlaying a porous membrane while the other utilizes a thick ECM hydrogel placed on a porous membrane. The thick hydrogel possesses a gradient of chemical cross-linking along its length to provide a softer substrate than that of the ECM film-coated membrane while maintaining mechanical stability.The monolayers on both platforms possessed goblet cells and abundant enterocytes and were impermeable to Lucifer yellow and fluorescein-dextran (70 kD) indicating high barrier integrity. Multiple transporter proteins were present in both primary-cell culture formats at levels similar to those present in freshly isolated crypts/villi; however, expression of breast cancer resistance protein (BCRP) and multidrug resistance protein 2 (MRP2) in the monolayers on the conventional scaffold was substantially less than that on the gradient cross-linked scaffold and freshly isolated crypts/villi. Monolayers on the conventional scaffold failed to transport the BCRP substrate prazosin while cells on the gradient cross-linked scaffold successfully transported this drug to better mimic the properties of in vivo small intestine.The results of this comparison highlight the need to create in vitro intestinal transport platforms whose characteristics mimic the in vivo lamina propria in order to accurately recapitulate epithelial function.}, journal={JOURNAL OF BIOLOGICAL ENGINEERING}, author={Speer, Jennifer E. and Gunasekara, Dulan B. and Wang, Yuli and Fallon, John K. and Attayek, Peter J. and Smith, Philip C. and Sims, Christopher E. and Allbritton, Nancy L.}, year={2019}, month={Apr} }
 @article{attayek_waugh_hunsucker_grayeski_sims_armistead_allbritton_2017, title={Automated microraft platform to identify and collect non-adherent cells successfully gene-edited with CRISPR-Cas9}, volume={91}, ISSN={["1873-4235"]}, DOI={10.1016/j.bios.2016.12.019}, abstractNote={Microraft arrays have been used to screen and then isolate adherent and non-adherent cells with very high efficiency and excellent viability; however, manual screening and isolation limits the throughput and utility of the technology. In this work, novel hardware and software were developed to automate the microraft array platform. The developed analysis software identified microrafts on the array with greater than 99% sensitivity and cells on the microrafts with 100% sensitivity. The software enabled time-lapse imaging and the use of temporally varying characteristics as sort criteria. The automated hardware released microrafts with 98% efficiency and collected released microrafts with 100% efficiency. The automated system was used to examine the temporal variation in EGFP expression in cells transfected with CRISPR-Cas9 components for gene editing. Of 11,499 microrafts possessing a single cell, 220 microrafts were identified as possessing temporally varying EGFP-expression. Candidate cells (n=172) were released and collected from the microraft array and screened for the targeted gene mutation. Two cell colonies were successfully gene edited demonstrating the desired mutation.}, journal={BIOSENSORS & BIOELECTRONICS}, author={Attayek, Peter J. and Waugh, Jennifer P. and Hunsucker, Sally A. and Grayeski, Philip J. and Sims, Christopher E. and Armistead, Paul M. and Allbritton, Nancy L.}, year={2017}, month={May}, pages={175–182} }
 @article{wang_gunasekara_attayek_reed_disalvo_nguyen_dutton_lebhar_bultman_sims_et al._2017, title={In Vitro Generation of Mouse Colon Crypts}, volume={3}, ISSN={["2373-9878"]}, DOI={10.1021/acsbiomaterials.7b00368}, abstractNote={Organoid culture has had a significant impact on in vitro studies of the intestinal epithelium; however, the exquisite architecture, luminal accessibility, and lineage compartmentalization found in vivo has not been recapitulated in the organoid systems. We have used a microengineered platform with suitable extracellular matrix contacts and stiffness to generate a self-renewing mouse colonic epithelium that replicates key architectural and physiological functions found in vivo, including a surface lined with polarized crypts. Chemical gradients applied to the basal-luminal axis compartmentalized the stem/progenitor cells and promoted appropriate lineage differentiation along the in vitro crypt axis so that the tissue possessed a crypt stem cell niche as well as a layer of differentiated cells covering the luminal surface. This new approach combining microengineered scaffolds, native chemical gradients, and biophysical cues to control primary epithelium ex vivo can serve as a highly functional and physiologically relevant in vitro tissue model.}, number={10}, journal={ACS BIOMATERIALS SCIENCE & ENGINEERING}, author={Wang, Yuli and Gunasekara, Dulan. B. and Attayek, Peter J. and Reed, Mark I. and DiSalvo, Matthew and Nguyen, Daniel L. and Dutton, Johanna S. and Lebhar, Michael S. and Bultman, Scott J. and Sims, Christopher E. and et al.}, year={2017}, month={Oct}, pages={2502–2513} }
 @article{attayek_hunsucker_sims_allbritton_armistead_2016, title={Identification and isolation of antigen-specific cytotoxic T lymphocytes with an automated microraft sorting system}, volume={8}, ISSN={["1757-9708"]}, DOI={10.1039/c6ib00168h}, abstractNote={The simultaneous measurement of T cell function with recovery of individual T cells would greatly facilitate characterizing antigen-specific responses bothin vivoand in model systems.}, number={12}, journal={INTEGRATIVE BIOLOGY}, author={Attayek, Peter J. and Hunsucker, Sally A. and Sims, Christopher E. and Allbritton, Nancy L. and Armistead, Paul M.}, year={2016}, pages={1208–1220} }
 @article{attayek_ahmad_wang_williamson_sims_magness_allbritton_2016, title={In vitro polarization of colonoids to create an intestinal stem cell compartment}, volume={11}, number={4}, journal={PLoS One}, author={Attayek, P. J. and Ahmad, A. A. and Wang, Y. L. and Williamson, I. and Sims, C. E. and Magness, S. T. and Allbritton, N. L.}, year={2016} }
 @article{attayek_hunsucker_wang_sims_armistead_allbritton_2015, title={Array-Based Platform To Select, Release, and Capture Epstein-Barr Virus-Infected Cells Based on Intercellular Adhesion}, volume={87}, ISSN={["1520-6882"]}, DOI={10.1021/acs.analchem.5b03579}, abstractNote={Microraft arrays were developed to select and separate cells based on a complex phenotype, weak intercellular adhesion, without knowledge of cell-surface markers or intracellular proteins. Since the cells were also not competent to bind to a culture surface, a method to encapsulate nonadherent cells within a gelatin plug on the concave microraft surface was developed, enabling release and collection of the cells without the need for cell attachment to the microraft surface. After microraft collection, the gelatin was liquified to release the cell(s) for culture or analysis. A semiautomated release and collection device for the microrafts demonstrated 100 ± 0% collection efficiency of the microraft while increasing throughput 5-fold relative to that of manual release and collection. Using the microraft array platform along with the gelatin encapsulation method, single cells that were not surface-attached were isolated with a 100 ± 0% efficiency and a 96 ± 4% postsort single-cell cloning efficiency. As a demonstration, Epstein-Barr virus-infected lymphoblastoid cell lines (EBV-LCL) were isolated based on their intercellular adhesive properties. The identified cell colonies were collected with a 100 ± 0% sorting efficiency and a postsort viability of 87 ± 3%. When gene expression analysis of the EBV latency-associated gene, EBNA-2, was performed, there was no difference in expression between blasting or weakly adhesive cells and nonblasting or nonadhesive cells. Microraft arrays are a versatile method enabling separation of cells based on complicated and as yet poorly understood cell phenotypes.}, number={24}, journal={ANALYTICAL CHEMISTRY}, author={Attayek, Peter J. and Hunsucker, Sally A. and Wang, Yuli and Sims, Christopher E. and Armistead, Paul M. and Allbritton, Nancy L.}, year={2015}, month={Dec}, pages={12281–12289} }
 @article{gach_attayek_whittlesey_yeh_allbritton_2014, title={Micropallet arrays for the capture, isolation and culture of circulating tumor cells from whole blood of mice engrafted with primary human pancreatic adenocarcinoma}, volume={54}, ISSN={["1873-4235"]}, DOI={10.1016/j.bios.2013.11.019}, abstractNote={Circulating tumor cells (CTCs) are important biomarkers of cancer progression and metastatic potential. The rarity of CTCs in peripheral blood has driven the development of technologies to isolate these tumor cells with high specificity; however, there are limited techniques available for isolating target CTCs following enumeration. A strategy is described to capture and isolate viable tumor cells from whole blood using an array of releasable microstructures termed micropallets. Specific capture of nucleated cells or cells expressing epithelial cell adhesion molecules (EpCAM) was achieved by functionalizing micropallet surfaces with either fibronectin, Matrigel or anti-EpCAM antibody. Surface grafting of poly(acrylic acid) followed by covalent binding of protein A/G enabled efficient capture of EpCAM antibody on the micropallet surface. MCF-7 cells, a human breast adenocarcinoma, were retained on the array surface with 90±8% efficiency when using an anti-EpCAM-coated array. To demonstrate the efficiency of tumor cell retention on micropallet arrays in the presence of blood, MCF-7 cells were mixed into whole blood and added to small arrays (71 mm2) coated with fibronectin, Matrigel or anti-EpCAM. These approaches achieved MCF-7 cell capture from ≤10 µL of whole blood with efficiencies greater than 85%. Furthermore, MCF-7 cells intermixed with 1 mL blood and loaded onto large arrays (7171 mm2) were captured with high efficiencies (≥97%), could be isolated from the array by a laser-based approach and were demonstrated to yield a high rate of colony formation (≥85%) after removal from the array. Clinical utility of this technology was shown through the capture, isolation and successful culture of CTCs from the blood of mice engrafted with primary human pancreatic tumors. Direct capture and isolation of living tumor cells from blood followed by analysis or culture will be a valuable tool for cancer cell characterization.}, journal={BIOSENSORS & BIOELECTRONICS}, author={Gach, Philip C. and Attayek, Peter J. and Whittlesey, Rebecca L. and Yeh, Jen Jen and Allbritton, Nancy L.}, year={2014}, month={Apr}, pages={476–483} }
 @article{gach_attayek_herrera_yeh_allbritton_2013, title={Isolation and in Vitro Culture of Rare Cancer Stem Cells from Patient-Derived Xenografts of Pancreatic Ductal Adenocarcinoma}, volume={85}, ISSN={["1520-6882"]}, DOI={10.1021/ac401165s}, abstractNote={Described is the construction of a large array of releasable microstructures (micropallets) along with screening and isolation protocols for sorting rare, approximately 1 in 10,000, cancer stem cells (CSCs) from a heterogeneous cell population. A 10.1 × 7.1 cm array of micropallets (50 × 50 × 75 μm structures and 25 μm micropallet gap) was fabricated on a large glass substrate, providing an array of approximately 1.3 million releasable microstructures. Image analysis algorithms were developed to permit array screening for identification of fluorescently labeled cells in less than 15 min using an epifluorescent wide-field microscope with a computer controlled translational stage. Device operation was tested by culturing HeLa cells transfected with green fluorescent protein (GFP) admixed with wild-type HeLa cells at ratios of 1:10(4) to 1:10(6) on the array followed by screening to identify flourescent cells. Micropallets containing cells of interest were then selectively released by a focused laser pulse and collected on a numbered poly(dimethylsiloxane) (PDMS) substrate with high viability. A direct comparison of this technology with fluorescence-activated cell sorting (FACS) demonstrated that micropallet arrays offered enhanced post sorting purity (100%), yield (100%), and viability (94-100%) for rare cell isolation. As a demonstration of the technology's value, pancreatic tumor cells from Panc-1 cell lines and patient-derived xenografts were screened for the presence of CD24, CD44, and CD326: surface markers of pancreatic CSCs. Following cell isolation and culture, 63 ± 23% of the isolated Panc-1 cells and 35% of sorted human xenograft cells formed tumor spheroids retaining high expression levels of CD24, CD44, and CD326. The ability to isolate rare cells from relatively small sample sizes will facilitate our understanding of cell biology and the development of new therapeutic strategies.}, number={15}, journal={ANALYTICAL CHEMISTRY}, author={Gach, Philip C. and Attayek, Peter J. and Herrera, Gabriela and Yeh, Jen Jen and Allbritton, Nancy L.}, year={2013}, month={Aug}, pages={7271–7278} }