Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing.

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatments. Focusing on gene expression, the transcriptomic market exploits the benefits of next-generation sequencing (NGS), leveraging RNA sequencing (RNA-seq) as standard for measuring genome-wide gene expression in biological samples. The cumbersome sample preparation, including RNA extraction, conversion to cDNA and amplification, prevents high-throughput translation of RNA-seq technologies. Bulk RNA barcoding and sequencing (BRB-seq) addresses this limitation by enabling sample preparation in multi-well plate format. Sample multiplexing combined with early pooling into a single tube reduces reagents consumption and manual steps. Enabling simultaneous pooling of all samples from the multi-well plate into one tube, our technology relies on smart labware: a pooling lid comprising fluidic features and small pins to transport the liquid, adapted to standard 96-well plates. Operated with standard fluidic tubes and pump, the system enables over 90% recovery of liquid in a single step in less than a minute. Large scale manufacturing of the lid is demonstrated with the transition from a milled polycarbonate/steel prototype into an injection molded polystyrene lid. The pooling lid demonstrated its value in supporting high-throughput barcode-based sequencing by pooling 96 different DNA barcodes directly from a standard 96-well plate, followed by processing within the single sample pool. This new pooling technology shows great potential to address medium throughput needs in the BRB-seq workflow, thereby addressing the challenge of large-scale and cost-efficient sample preparation for RNA-seq.

Clinical Controversy in Transplantation: Tacrolimus Versus Cyclosporine in Statin Drug Interactions.

Objective: To review the available literature that provides evidence for the absence of statin interactions with tacrolimus compared with cyclosporine. Data Sources: A literature search of PubMed was performed (1990 to June 2019) using the following search terms: calcineurin inhibitors, tacrolimus, cyclosporine, statins, atorvastatin, simvastatin, and drug interactions. Clinical practice guidelines, article bibliographies, drug interaction database references, and product monographs were also reviewed. Study Selection and Data Extraction: Relevant English-language studies describing the mechanism of interaction, the magnitude of pharmacokinetic alterations, and safety were evaluated. In vitro data and studies conducted in adult humans were considered. Data Synthesis: Studies demonstrate pharmacokinetic differences between cyclosporine and tacrolimus, particularly with regard to inhibition of 2 hepatic transporters: P-glycoprotein and organic anion transporting polypeptide (OATP). Compared with cyclosporine, tacrolimus does not affect these transporters, does not enhance statin exposure, and does not increase statin-associated safety events. Relevance to Patient Care and Clinical Practice: Clinical practice guidelines allude to the need to reduce statin doses in the setting of tacrolimus. Some providers have adopted this practice, and doing so may prevent transplant recipients from attaining cardiovascular benefit, especially when increased or high-intensity doses are required. The pharmacokinetic differences between tacrolimus and cyclosporine highlight different interaction potential with statins. Conclusions: Clinicians need to be aware that tacrolimus and cyclosporine are not the same with regard to causing drug interactions with statins. Tacrolimus can be used with statins without the need for dose adjustments because of lack of an interaction.

High-content, cell-by-cell assessment of HER2 overexpression and amplification: a tool for intratumoral heterogeneity detection in breast cancer.

Immunohistochemistry and fluorescence in situ hybridization are the two standard methods for human epidermal growth factor receptor 2 (HER2) assessment. However, they have severe limitations to assess quantitatively intratumoral heterogeneity (ITH) when multiple subclones of tumor cells co-exist. We develop here a high-content, quantitative analysis of breast cancer tissues based on microfluidic experimentation and image processing, to characterize both HER2 protein overexpression and HER2 gene amplification at the cellular level. The technique consists of performing sequential steps on the same tissue slide: an immunofluorescence (IF) assay using a microfluidic protocol, an elution step for removing the IF staining agents, a standard FISH staining protocol, followed by automated quantitative cell-by-cell image processing. Moreover, ITH is accurately detected in both cluster and mosaic form using an analysis of spatial association and a mathematical model that allows discriminating true heterogeneity from artifacts due to the use of thin tissue sections. This study paves the way to evaluate ITH with high accuracy and content while requiring standard staining methods.

Enhancing patient engagement and blood pressure management for renal transplant recipients via home electronic monitoring and web-enabled collaborative care.

BACKGROUND: Effective management of hypertension in chronic kidney disease and renal transplantation is a clinical priority and has societal implications in terms of preserving and optimizing the value of scarce organs. However, hypertension is optimally managed in only 37% of people with chronic kidney disease, and poor control can contribute to premature graft loss in renal transplant recipients. This article describes a telehealth system that incorporates home electronic blood pressure (BP) monitoring and uploading to a patient portal coupled with a Web-based dashboard that enables clinical pharmacist collaborative care in a renal transplant clinic. MATERIALS AND METHODS: The telehealth system was developed and implemented as a quality improvement initiative in a renal transplant clinic in a large, 700-bed, urban hospital with the aim of improving BP in posttransplant patients. A convenience sample of 66 posttransplant patients was recruited by the clinical pharmacist from consecutive referrals to the Transplant Clinic. RESULTS: Preliminary results show statistically significant reductions in average systolic and diastolic BP of 6.0 mm Hg and 3.0 mm Hg, respectively, at 30 days after enrollment. Two case reports describe the instrumental role of home BP monitoring in the context of medication therapy management. CONCLUSIONS: Optimizing BP control for both pre- and post-renal transplant patients is likely to benefit society in terms of preserving scarce resources and reducing healthcare costs due to premature graft failure. Connected health systems hold great promise for supporting team-based care and improved health outcomes.

Aperture-Controlled Fabrication of All-Dielectric Structural Color Pixels.

While interference colors have been known for a long time, conventional color filters have large spatial dimensions and cannot be used to create compact pixelized color pictures. Here we report a simple yet elegant interference-based method of creating microscopic structural color pixels using a single-mask process using standard UV photolithography on an all-dielectric substrate. The technology makes use of the varied aperture-controlled physical deposition rate of low-temperature silicon dioxide inside a hollow cavity to create a thin-film stack with the controlled bottom layer thickness. The stack defines which wavelengths of the reflected light interfere constructively, and thus the cavities act as micrometer-scale pixels of a predefined color. Combinations of such pixels produce vibrant colorful pictures visible to the naked eye. Being fully CMOS-compatible, wafer-scale, and not requiring costly electron-beam lithography, such a method paves the way toward large scale applications of structural colors in commercial products.

Coplanar embedding of multiple 3D cell models in hydrogel towards high-throughput micro-histology.

Standardised and high-throughput methods have been developed for the production and experimental handling of some 3D in vitro models. However, adapted analytical tools are still missing for scientists and researchers to fully exploit the potential of complex cellular models in pre-clinical drug testing and precision medicine. Histology is the established, cost-effective and gold standard method for structural and functional tissue analysis. However, standard histological processes are challenging and costly to apply to 3D cell models, as their small size often leads to poor alignment of samples, which lowers analysis throughput. This body of work proposes a new approach: HistoBrick facilitates histological processing of spheroids and organoids by enabling gel embedding of 3D cell models with precise coplanar alignment, parallel to the sectioning plane, thus minimising the loss of sample material. HistoBrick's features are compatible with automation standards, potentially allowing automated sample transfer from a multi-well plate to the gel device. Moreover, HistoBrick's technology was validated by demonstrating the alignment of HepG2 cultured spheroids measuring 150-200 µm in diameter with a height precision of ± 80 µm. HistoBrick allows up to 96 samples to be studied across minimal sections, paving the way towards high-throughput micro-histology.

Planar hydrodynamic traps and buried channels for bead and cell trapping and releasing.

We present a novel concept for the controlled trapping and releasing of beads and cells in a PDMS microfluidic channel without obstacles present around the particle or in the channel. The trapping principle relies on a two-level microfluidic configuration: a top main PDMS channel interconnected to a buried glass microchannel using round vias. As the fluidic resistances rule the way the liquid flows inside the channels, particles located in the streamlines passing inside the buried level are immobilized by the round via with a smaller diameter, leaving the object motionless in the upper PDMS channel. The particle is maintained by the difference of pressure established across its interface and acts as an infinite fluidic resistance, virtually cancelling the subsequent buried fluidic path. The pressure is controlled at the outlet of the buried path and three modes of operation of a trap are defined: idle, trapping and releasing. The pressure conditions for each mode are defined based on the hydraulic-electrical circuit equivalence. The trapping of polystyrene beads in a compact array of 522 parallel traps controlled by a single pressure was demonstrated with a trapping efficiency of 94%. Pressure conditions necessary to safely trap cells in holes of different diameters were determined and demonstrated in an array of 25 traps, establishing the design and operation rules for the use of planar hydrodynamic traps for biological assays.

Use of Eculizumab in Transplant-Associated Thrombotic Microangiopathy in a Patient With Polycystic Kidney Disease Immediately Post-Kidney Transplant: A Case Report.

Transplant-associated thrombotic microangiopathy (TMA) in the post-organ transplantation setting occurs from a number of potential inciting factors, such as the use of calcineurin inhibitors, ischemic injury, infections, or antibody-mediated rejection leading to unchecked complement activation and end-organ damage. Delayed recognition of this condition can result in allograft loss. In this case description, we describe the first case of de novo TMA in a patient with polycystic kidney disease that occurred immediately after kidney transplantation. The diagnosis was made promptly on the basis of clinical and laboratory characteristics by a multidisciplinary team and confirmed through kidney biopsy, which showed acute TMA. The patient was successfully managed by replacing tacrolimus with belatacept, which targets cytotoxic T lymphocyte antigen 4, and use of eculizumab, a C5 inhibitor. Eculizumab treatment was discontinued after 3 months of complement inhibition on the patient's request, and relapse of TMA has not been encountered after more than 1 year of follow-up.

Structural transitions and mechanochemical coupling in the nucleoprotein filament explain homology selectivity and Rad51 protein cooperativity in cellular DNA repair.

The nucleoprotein filament (NPF) is the fundamental element of homologous recombination (HR), a major mechanism for the repair of double-strand DNA breaks in the cell. The NPF is made of the damaged DNA strand surrounded by recombinase proteins, and its sensitivity to base-pairing mismatches is a crucial feature that guarantees the fidelity of the repair. The concurrent recombinases are also essential for several steps of HR. In this work, we used torque-sensitive magnetic tweezers to probe and apply mechanical constraints to single nucleoprotein filaments (NPFs). We demonstrated that the NPF undergoes structural transitions from a stretched to a compact state, and we measured the corresponding mechanochemical signatures. Using an active two-state model, we proposed a free-energy landscape for the NPF transition. Using this quantitative model, we explained both how the sensitivity of the NPF to the homology length is regulated by its structural transition and how the cooperativity of Rad51 favors selectivity to relatively long homologous sequences.

Microfluidics-assisted multiplexed biomarker detection for in situ mapping of immune cells in tumor sections.

Because of the close interaction between tumors and the immune system, immunotherapies are nowadays considered as the most promising treatment against cancer. In order to define the diagnosis and the subsequent therapy, crucial information about the immune cells at the tumor site is needed. Indeed, different types or activation status of cells may be indicative for specific and personalized treatments. Here, we present a quantitative method to identify ten different immuno-markers in the same tumor cut section, thereby saving precious samples and enabling correlative analysis on several cell families and their activation status in a tumor microenvironment context. We designed and fabricated a microfluidic chip with optimal thermomechanical and optical properties for fast delivery of reagents on tissue slides and for fully automatic imaging by integration with an optical microscope. The multiplexing capability of the system is enabled by an optimized cyclic immunofluorescence protocol, with which we demonstrated quantitative sequential immunostaining of up to ten biomarkers on the same tissue section. Furthermore, we developed high-quality image-processing algorithms to map each cell in the entire tissue. As proof-of-concept analyses, we identified coexpression and colocalization patterns of biomarkers to classify the immune cells and their activation status. Thanks to the quantitativeness and the automation of both the experimental and analytical methods, we believe that this multiplexing approach will meet the increasing clinical need of personalized diagnostics and therapy in cancer pathology.

Assessing the Potential Deployment of Biosensors for Point-of-Care Diagnostics in Developing Countries: Technological, Economic and Regulatory Aspects.

Infectious diseases and antimicrobial resistance are major burdens in developing countries, where very specific conditions impede the deployment of established medical infrastructures. Since biosensing devices are nowadays very common in developed countries, particularly in the field of diagnostics, they are at a stage of maturity at which other potential outcomes can be explored, especially on their possibilities for multiplexing and automation to reduce the time-to-results. However, the translation is far from being trivial. In order to understand the factors and barriers that can facilitate or hinder the application of biosensors in resource-limited settings, we analyze the context from several angles. First, the technology of the devices themselves has to be rethought to take into account the specific needs and the available means of these countries. For this, we describe the partition of a biosensor into its functional shells, which define the information flow from the analyte to the end-user, and by following this partition we assess the strengths and weaknesses of biosensing devices in view of their specific technological development and challenging deployment in low-resource environments. Then, we discuss the problem of cost reduction by pointing out transversal factors, such as throughput and cost of mistreatment, that need to be re-considered when analyzing the cost-effectiveness of biosensing devices. Beyond the technical landscape, the compliance with regulations is also a major aspect that is described with its link to the validation of the devices and to the acceptance from the local medical personnel. Finally, to learn from a successful case, we analyze a breakthrough inexpensive biosensor that is showing high potential with respect to many of the described aspects. We conclude by mentioning both some transversal benefits of deploying biosensors in developing countries, and the key factors that can drive such applications.

Combining fluorescence-based image segmentation and automated microfluidics for ultrafast cell-by-cell assessment of biomarkers for HER2-type breast carcinoma.

Immunohistochemistry (IHC) is one of the main clinical techniques for biomarker assessment on tissue biopsies. It consists in chromogenic labeling with specific antibodies, followed by optical imaging, and it is used for diagnosis and therapeutic targeting. A well-known drawback of IHC is its limited robustness, which often precludes quantitative biomarker assessment. We combine microfluidic immunostaining, fluorescence imaging, and image-based cell segmentation to create an ultrafast procedure for accurate biomarker assessment via IHC. The experimental protocol is very simple and based on fast delivery of reagents in a microfluidic chamber created by clamping a half-chamber patterned in a silicon chip on top of a tumor tissue section. Also, the imaging procedure simply requires a standard fluorescence microscope, already widely used in clinical practice. The image processing is based on local-contrast enhancement and thresholding of the obtained fluorescence image, with subsequent Voronoi segmentation. To assess the experimental and analytical procedure on robust biological controls, we apply our method to well-characterized cell lines, which guarantee higher reproducibility than whole-tissue samples and therefore enable to disentangle the technical variability from the biological variability. To increase the potential translationality, we address the detection and quantification of the human epidermal growth factor receptor 2 (HER2) protein, which is a biomarker for HER2-type breast carcinoma diagnosis and therapy. We report both ultrafast immunofluorescence staining (5 min per sample) of two breast cancer biomarkers and ultrafast cell segmentation (1 min per sample = processing of thousands of cells). This provides a quantitative, cell-based immunofluorescent signal, with which we propose a potential diagnostic criterion to separate HER2-positive and HER2-negative breast cancer cells at high sensitivity and specificity.

Microsphere-mediated optical contrast tuning for designing imaging systems with adjustable resolution gain.

Upon illumination, a dielectric microsphere (µS) can generate a photonic nanojet (PNJ), which plays a role in the super-resolution imaging of a sample placed in the µS's immediate proximity. Recent microscopy implementations pioneered this concept but, despite the experimental characterization and theoretical modeling of the PNJ, the key physical factors that enable optimization of such imaging systems are still debated. Here, we systematically analyzed the parameters that govern the resolution increase in the case of large-diameter (>20 µm) µS-assisted incoherent microscopy by studying both the illumination and the detection light paths. We determined the enhanced-resolution zone created by the µS, in which the detection system has a net resolution gain that we calculated theoretically and subsequently confirmed experimentally. Our results quantitatively describe the resolution enhancement mediated by the optical contrast between the µS and its surrounding medium, and provide concrete means for designing µS-enhanced imaging systems for several application requirements.

Multimodal imaging and high-throughput image-processing for drug screening on living organisms on-chip.

A major step for the validation of medical drugs is the screening on whole organisms, which gives the systemic information that is missing when using cellular models. Caenorhabditis elegans is a soil worm that catches the interest of researchers who study systemic physiopathology (e.g., metabolic and neurodegenerative diseases) because: (1) its large genetic homology with humans supports translational analysis; (2) worms are much easier to handle and grow in large amounts compared with rodents, for which (3) the costs and (4) the ethical concerns are substantial. Here, we demonstrate how multimodal optical imaging on such an organism can provide high-content information relevant to the drug development pipeline (e.g., mode-of-action identification, dose-response analysis), especially when combined with on-chip multiplexing capability. After designing a microfluidic array to select small separated populations of C. elegans, we combine fluorescence and bright-field imaging along with high-throughput feature recognition and signal detection to enable the identification of the mode-of-action of an antibiotic. For this purpose, we use a genetically encoded fluorescence reporter of mitochondrial stress, which we studied in living specimens during their entire development. Furthermore, we demonstrate real-time, very large field-of-view capability on multiplexed motility assays for the assessment of the dose-response relation of an anesthetic.

Achieving blood pressure control among renal transplant recipients by integrating electronic health technology and clinical pharmacy services.

PURPOSE: The implementation and outcomes of a program combining electronic home blood pressure monitoring (HBPM) and pharmacist-provided medication therapy management (MTM) services in a renal transplantation clinic are described. SUMMARY: Patients enrolled in the program were provided with a computer-enabled blood pressure monitor. A dedicated renal transplantation pharmacist was integrated into the renal transplantation team under a collaborative care practice agreement. The collaborative care agreement allowed the pharmacist to authorize medication additions, deletions, and dosage changes. Comprehensive disease and blood pressure education was provided by a clinical pharmacist. In the pretransplantation setting, the pharmacist interviewed the renal transplant candidate and documents allergies, verified the patient's medication profile, and identified and assessed barriers to medication adherence. A total of 50 renal transplant recipients with at least one recorded home blood pressure reading and at least one year of follow-up were included in our analysis. A significant reduction in mean systolic and diastolic blood pressure values were observed at 30, 90, 180, and 360 days after enrollment in the program (p < 0.05). Pharmacist interventions were documented for 37 patients. Medication-related problems accounted for 46% of these interventions and included dosage modifications, regimen changes, and mitigation of barriers to medication access and adherence. CONCLUSION: Implementation of electronic HBPM and pharmacist-provided MTM services implemented in a renal transplant clinic was associated with sustained improvements in blood pressure control. Incorporation of a pharmacist in the renal transplant clinic resulted in the detection and resolution of medication-related problems.

SwissPalm: Protein Palmitoylation database.

Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm ( http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

Optical detection and sizing of single nanoparticles using continuous wetting films.

The physical interaction between nanoscale objects and liquid interfaces can create unique optical properties, enhancing the signatures of the objects with subwavelength features. Here we show that the evaporation on a wetting substrate of a polymer solution containing submicrometer or nanoscale particles creates liquid microlenses that arise from the local deformations of the continuous wetting film. These microlenses have properties similar to axicon lenses that are known to create beams with a long depth of focus. This enhanced depth of focus allows detection of single nanoparticles using a low-magnification microscope objective lens, achieving a relatively wide field-of-view, while also lifting the constraints on precise focusing onto the object plane. Hence, by creating these liquid axicon lenses through spatial deformations of a continuous thin wetting film, we transfer the challenge of imaging individual nanoparticles to detecting the light focused by these lenses. As a proof of concept, we demonstrate the detection and sizing of single nanoparticles (100 and 200 nm), CpGV granuloviruses, as well as Staphylococcus epidermidis bacteria over a wide field-of-view of 5.10 × 3.75 mm(2) using a 5× objective lens with a numerical aperture of 0.15. In addition to conventional lens-based microscopy, this continuous wetting-film-based approach is also applicable to lens-free computational on-chip imaging, which can be used to detect single nanoparticles over a large field-of-view of >20-30 mm(2). These results could be especially useful for high-throughput field analysis of nanoscale objects using compact and cost-effective microscope designs.