Barcoded multiple displacement amplification for high coverage sequencing in spatial genomics.

Determining mutational landscapes in a spatial context is essential for understanding genetically heterogeneous cell microniches. Current approaches, such as Multiple Displacement Amplification (MDA), offer high genome coverage but limited multiplexing, which hinders large-scale spatial genomic studies. Here, we introduce barcoded MDA (bMDA), a technique that achieves high-coverage genomic analysis of low-input DNA while enhancing the multiplexing capabilities. By incorporating cell barcodes during MDA, bMDA streamlines library preparation in one pot, thereby overcoming a key bottleneck in spatial genomics. We apply bMDA to the integrative spatial analysis of triple-negative breast cancer tissues by examining copy number alterations, single nucleotide variations, structural variations, and kataegis signatures for each spatial microniche. This enables the assessment of subclonal evolutionary relationships within a spatial context. Therefore, bMDA has emerged as a scalable technology with the potential to advance the field of spatial genomics significantly.

Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches.

Epitranscriptomic features, such as single-base RNA editing, are sources of transcript diversity in cancer, but little is understood in terms of their spatial context in the tumour microenvironment. Here, we introduce spatial-histopathological examination-linked epitranscriptomics converged to transcriptomics with sequencing (Select-seq), which isolates regions of interest from immunofluorescence-stained tissue and obtains transcriptomic and epitranscriptomic data. With Select-seq, we analyse the cancer stem cell-like microniches in relation to the tumour microenvironment of triple-negative breast cancer patients. We identify alternative splice variants, perform complementarity-determining region analysis of infiltrating T cells and B cells, and assess adenosine-to-inosine base editing in tumour tissue sections. Especially, in triple-negative breast cancer microniches, adenosine-to-inosine editome specific to different microniche groups is identified.

One-step assembly of barcoded planar microparticles for efficient readout of multiplexed immunoassay.

Barcoded planar microparticles are suitable for developing cost-efficient multiplexed assays, but the robustness and efficiency of the readout process still needs improvement. Here, we designed a one-step microparticle assembling chip that produces efficient and accurate multiplex immunoassay readout results. Our design was also compatible with injection molding for mass production.

Recent Advances in Polymer Additive Engineering for Diagnostic and Therapeutic Hydrogels.

Hydrogels are hydrophilic polymer materials that provide a wide range of physicochemical properties as well as are highly biocompatible. Biomedical researchers are adapting these materials for the ever-increasing range of design options and potential applications in diagnostics and therapeutics. Along with innovative hydrogel polymer backbone developments, designing polymer additives for these backbones has been a major contributor to the field, especially for expanding the functionality spectrum of hydrogels. For the past decade, researchers invented numerous hydrogel functionalities that emerge from the rational incorporation of additives such as nucleic acids, proteins, cells, and inorganic nanomaterials. Cases of successful commercialization of such functional hydrogels are being reported, thus driving more translational research with hydrogels. Among the many hydrogels, here we reviewed recently reported functional hydrogels incorporated with polymer additives. We focused on those that have potential in translational medicine applications which range from diagnostic sensors as well as assay and drug screening to therapeutic actuators as well as drug delivery and implant. We discussed the growing trend of facile point-of-care diagnostics and integrated smart platforms. Additionally, special emphasis was given to emerging bioinformatics functionalities stemming from the information technology field, such as DNA data storage and anti-counterfeiting strategies. We anticipate that these translational purpose-driven polymer additive research studies will continue to advance the field of functional hydrogel engineering.

PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing.

Spatial mapping of genomic data to tissue context in a high-throughput and high-resolution manner has been challenging due to technical limitations. Here, we describe PHLI-seq, a novel approach that enables high-throughput isolation and genome-wide sequence analysis of single cells or small numbers of cells to construct genomic maps within cancer tissue in relation to the images or phenotypes of the cells. By applying PHLI-seq, we reveal the heterogeneity of breast cancer tissues at a high resolution and map the genomic landscape of the cells to their corresponding spatial locations and phenotypes in the 3D tumor mass.

Self-organization of maze-like structures via guided wrinkling.

Sophisticated three-dimensional (3D) structures found in nature are self-organized by bottom-up natural processes. To artificially construct these complex systems, various bottom-up fabrication methods, designed to transform 2D structures into 3D structures, have been developed as alternatives to conventional top-down lithography processes. We present a different self-organization approach, where we construct microstructures with periodic and ordered, but with random architecture, like mazes. For this purpose, we transformed planar surfaces using wrinkling to directly use randomly generated ridges as maze walls. Highly regular maze structures, consisting of several tessellations with customized designs, were fabricated by precisely controlling wrinkling with the ridge-guiding structure, analogous to the creases in origami. The method presented here could have widespread applications in various material systems with multiple length scales.

Fiber composite slices for multiplexed immunoassays.

Fabrication methods for the development of multiplexed immunoassay platforms primarily depend on the individual functionalization of reaction chambers to achieve a heterogeneous reacting substrate composition, which increases the overall manufacturing time and cost. Here, we describe a new type of low-cost fabrication method for a scalable immunoassay platform based on cotton threads. The manufacturing process involves the fabrication of functionalized fibers and the arrangement of these fibers into a bundle; this bundle is then sectioned to make microarray-like particles with a predefined surface architecture. With these sections, composed of heterogeneous thread fragments with different types of antibodies, we demonstrated quantitative and 7-plex immunoassays. We expect that this methodology will prove to be a versatile, low-cost, and highly scalable method for the fabrication of multiplexed bioassay platforms.

Biomimetic microfingerprints for anti-counterfeiting strategies.

An unclonable, fingerprint-mimicking anti-counterfeiting strategy is presented that encrypts polymeric particles with randomly generated silica film wrinkles. The generated wrinkle codes are as highly unique as human fingerprints and are technically irreproducible. Superior to previous physical unclonable functions, codes are tunable on demand and generable on various geometries. Reliable authentication of real-world products that have these microfingerprints is demonstrated using optical decoding methods.

Potentiometric multichannel cytometer microchip for high-throughput microdispersion analysis.

The parallelization of microfluidic cytometry is expected to lead to considerably enhanced throughput enabling point-of-care diagnosis. In this article, the development of a microfluidic potentiometric multichannel cytometer is presented. Parallelized microfluidic channels sharing a fluid path inevitably suffer from interchannel signal crosstalk that results from electrical coupling within the microfluidic channel network. By employing three planar electrodes within a single detection channel, we electrically decoupled each channel unit, thereby enabling parallel analysis by using a single cytometer microchip with multiple microfluidic channels. The triple-electrode configuration is validated by analyzing the size and concentration of polystyrene microbeads (diameters: 1.99, 2.58, 3, and 3.68 µm; concentration range: ∼2 × 10(5) mL(-1) to ∼1 × 10(7) mL(-1)) and bacterial microdispersion samples (Bacillus subtilis, concentration range: ∼4 × 10(5) CFU mL(-1) to ∼3 × 10(6) CFU mL(-1)). Crosstalk-free parallelized analysis is then demonstrated using a 16-channel potentiometric cytometer (maximum cross-correlation coefficients |r|: < 0.13 in all channel combinations). A detection throughput of ∼48,000 s(-1) was achieved; the throughout can be easily increased with the degree of parallelism of a single microchip without additional technical complexities. Therefore, this methodology should enable high-throughput and low-cost cytometry.