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.

Integrated elastomer-based device for measuring the mechanics of adherent cell monolayers.

Cells in the body collectively sustain mechanical deformations in almost all physiological functions. From the morphogenesis stage, cells' ability to sustain stress is essential for the body's well-being. Several pathologies have been associated with abnormal mechanical properties, thus suggesting the Young's modulus as a biomarker to diagnose diseases and determine their progression. Advancements in the field are quite slow because current techniques for measuring cell and tissue mechanics rely on complex and bulky measurement platforms that have low repeatability rates and limited measurement time-scales. We present the first miniaturized system that allows accurate quantification of the Young's modulus of adherent cell monolayers over a longer time (1-2 days). Our approach is based on tensile testing and optical read-out. Thanks to a thoughtful design and material choice, we are able to miniaturize tensile testing platforms into a 1 cm × 2 cm device. We provide highly repeatable Young's modulus measurements in the relevant range between 3 kPa and 300 kPa, over time and under physiological conditions, thus representing an interesting alternative to existing measurement platforms. Furthermore, the compatibility with standard biological equipment, continuous optical imaging and measurements on all types of adherent cells make this device highly versatile. Measurements on human sarcoma osteogenic (SaOS2) and Madin-Darby canine kidney cells (MDCK) are reported. The demonstrated capability to measure real-time changes in mechanical properties, such as after chemical treatment, opens the door for investigating the effects of drugs on cell mechanics.

Parallel AFM imaging and force spectroscopy using two-dimensional probe arrays for applications in cell biology.

Atomic force microscopy (AFM) investigations of living cells provide new information in both biology and medicine. However, slow cell dynamics and the need for statistically significant sample sizes mean that data collection can be an extremely lengthy process. We address this problem by parallelizing AFM experiments using a two-dimensional cantilever array, instead of a single cantilever. We have developed an instrument able to operate a two-dimensional cantilever array, to perform topographical and mechanical investigations in both air and liquid. Deflection readout for all cantilevers of the probe array is performed in parallel and online by interferometry. Probe arrays were microfabricated in silicon nitride. Proof-of-concept has been demonstrated by analyzing the topography of hard surfaces and fixed cells in parallel, and by performing parallel force spectroscopy on living cells. These results open new research opportunities in cell biology by measuring the adhesion and elastic properties of a large number of cells. Both properties are essential parameters for research in metastatic cancer development.

Integrated optical biosensor for in-line monitoring of cell cultures.

An analytical detection platform was developed to evaluate the induced toxicity in cell cultures exposed to foreign agents like growth factors or nanoparticles. Connecting a biosensing detection device to the cell culture flasks allows analyzing the composition of cell medium in real-time. The analysis relies on the quantification of inflammatory cytokines released by cells into the cell culture medium, by means of solid-phase immunoassays analyzed with the wavelength interrogated optical sensing (WIOS) instrument. A fluidic system for in situ measurements allows detecting cytokines in real-time, with a sensitivity of 1-100 ng/mL depending on the cytokine. In addition, integration of an in-line optical absorbance measurement unit, in combination with the standard AB cell proliferation assay, provides information on the cell viability in the culture. Fluidic connections between the cell culture flasks, the optical biosensor and the absorbance measurement unit simultaneously allow quantifying up to three cytokines (interleukin 8, interleukin 6 and the monocyte chemotactic protein), assessing cellular proliferation, and thus discriminating between naïve cells and cells exposed to foreign agents such as growth factors (tumor necrosis factor alpha) or nanoparticles. This analytical tool presents a high potential for assessing the cytotoxicity of nanoparticles and other chemicals in vitro.