Spatially Resolved CRISPR Screen Sequencing via Perturb-DBiT.

Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for simultaneous co-sequencing of spatial transcriptome and guide RNAs (gRNAs) on the same tissue section for in vivo CRISPR screen with genome-scale gRNA libraries, offering a comprehensive understanding of how genetic modifications affect cellular behavior and tissue architecture. This platform supports a variety of delivery vectors, gRNA library sizes, and tissue preparations, along with two distinct gRNA capture methods, making it adaptable to a wide range of experimental setups.

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues.

The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for 5 years.

Chromatin conformation and histone modification profiling across human kidney anatomic regions.

The three major anatomic regions of the human kidney include the cortex, medulla and papilla, with different functions and vulnerabilities to kidney diseases. Epigenetic mechanisms underlying these anatomic structures are incompletely understood. Here, we performed chromatin conformation capture with Hi-C and histone modification H3K4me3/H3K27me3 Cleavage Under Targets and Release Using Nuclease (CUT&RUN) sequencing on the kidney cortex, medulla and papilla dissected from one individual donor.

Protocol for multimodal profiling of human kidneys with simultaneous high-throughput ATAC and RNA expression with sequencing.

Simultaneous high-throughput ATAC and RNA expression with sequencing (SHARE-seq) profiles transcriptomics and chromatin accessibility in the same cells at high throughput. Here, we present a protocol for multimodal profiling of human kidneys with SHARE-seq. We describe steps for processing fixed nuclei for SHARE-seq split-pool barcoding and library preparation.

Spatially resolved metabolomic dataset of distinct human kidney anatomic regions.

Cortex, medulla and papilla are three major human kidney anatomic structures and they harbour unique metabolic functions, but the underlying metabolomic profiles are largely unknown at spatial resolution. Here, we generated a spatially resolved metabolomics dataset on human kidney cortex, medulla and papilla tissues dissected from the same donor. Matrix-Assisted Laser Desorption/Ionization-Imaging Mass Spectrometry (MALDI-IMS) was used to detect metabolite species over mass-to-charge ratios of 50 -1500 for each section at a resolution of 10 × 10 µm pixel size.

Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy.

A large-scale multimodal atlas that includes major kidney regions is lacking. Here, we employed simultaneous high-throughput single-cell ATAC/RNA sequencing (SHARE-seq) and spatially resolved metabolomics to profile 54 human samples from distinct kidney anatomical regions. We generated transcriptomes of 446,267 cells and chromatin accessibility profiles of 401,875 cells and developed a package to analyze 408,218 spatially resolved metabolomes.

Targeting de novo lipogenesis to mitigate kidney disease.

Ten percent of the population worldwide suffers from chronic kidney disease (CKD), but the mechanisms driving CKD pathology are incompletely understood. While dysregulated lipid metabolism is one hallmark of CKD, the pathogenesis of cellular lipid accumulation remains unclear. In this issue of the JCI, Mukhi et al.

Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease.

Background: Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and chronic kidney disease.

Results: The likelihood of a cell having LOY varies depending on its location in the nephron.

Proteomic Portrait of Human Lymphoma Reveals Protein Molecular Fingerprint of Disease Specific Subtypes and Progression.

Unlabelled: An altered proteome in lymph nodes often suggests abnormal signaling pathways that may be associated with diverse lymphatic disorders. Current clinical biomarkers for histological classification of lymphomas have encountered many discrepancies, particularly for borderline cases. Therefore, we launched a comprehensive proteomic study aimed to establish a proteomic landscape of patients with various lymphatic disorders and identify proteomic variations associated with different disease subgroups.

Hyperbranched Conjugated Polymer with Multiple Charge Transfer Enables High-Efficiency Nondoped Red Electroluminescence with Low Driving Voltage.

Conjugated polymers featuring thermally activated delayed fluorescence (TADF) attract tremendous attention in both academic and industry communities due to their easy solution processing for fabricating large-area and low-cost high-performance polymer light-emitting diodes (PLEDs). However, current nondoped solution-processed PLEDs frequently encounter significant efficiency roll-offs and unreasonably high operating voltages at high brightness, especially for red-emitting polymers. Herein, we design hyperbranched conjugated polymers (HCPs) with D-A-D type TADF characteristics for high-performance red-emitting PLEDs.

Mouse kidney nuclear isolation and library preparation for single-cell combinatorial indexing RNA sequencing.

Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq3) enables high-throughput single-nucleus transcriptomic profiling of multiple samples in one experiment. Here, we describe an optimized protocol of mouse kidney nuclei isolation and sci-RNA-seq3 library preparation. The use of a dounce tissue homogenizer enables nuclei extraction with high yield.

Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis.

The underlying cellular events driving kidney fibrogenesis and metabolic dysfunction are incompletely understood. Here, we employed single-cell combinatorial indexing RNA sequencing to analyze 24 mouse kidneys from two fibrosis models. We profiled 309,666 cells in one experiment, representing 50 cell types/states encompassing epithelial, endothelial, immune, and stromal populations.

Single Cell Technologies: Beyond Microfluidics.

Single-cell RNA-sequencing (scRNA-seq) has been widely adopted in recent years due to standardized protocols and automation, reliability, and standardized bioinformatic pipelines. The most widely adopted platform is the 10× Genomics solution. Although powerful, this system is limited by its high cost, moderate throughput, and the inability to customize due to fixed kit components.

A sensitive fluorescent sensor for the detection of trace water in organic solvents based on carbon quantum dots with yellow fluorescence.

The quantitative analysis of trace water in organic solvents has always been a research hotspot, and it is still in the development stage and needs to be continuously developed. In this study, a facile and rapid approach was developed for the preparation of carbon quantum dots (CQDs) with yellow fluorescence emission and ultrahigh absolute fluorescence quantum yields (92.6%).

Pluronic-encapsulated natural chlorophyll nanocomposites for in vivo cancer imaging and photothermal/photodynamic therapies.

A great challenge in developing nanotechnologies for cancer diagnosis and therapy has been the combined functionalities required for complicated clinical procedures. Among all requirements, toxicity has been the major hurdle that has prevented most of the nano-carriers from clinical use. Here, we extracted chlorophyll (Chl) from vegetable and encapsulated it into polymer (pluronic F68, Plu) micelles for cancer imaging and therapy.

Irreversible denaturation of proteins through aluminum-induced formation of backbone ring structures.

A combination of ab initio calculations, circular dichroism, nuclear magnetic resonance, and X-ray photoelectron spectroscopy has shown that aluminum ions can induce the formation of backbone ring structures in a wide range of peptides, including neurodegenerative disease related motifs. These ring structures greatly destabilize the protein and result in irreversible denaturation. This behavior benefits from the ability of aluminum ions to form chemical bonds simultaneously with the amide nitrogen and carbonyl oxygen atoms on the peptide backbone.

Near-infrared laser light mediated cancer therapy by photothermal effect of Fe3O4 magnetic nanoparticles.

The photothermal effect of Fe3O4 magnetic nanoparticles is investigated for cancer therapy both in vitro and in vivo experiments. Heat is found to be rapidly generated by red and near-infrared (NIR) range laser irradiation of Fe3O4 nanoparticles with spherical, hexagonal and wire-like shapes. These Fe3O4 nanoparticles are coated with carboxyl-terminated poly (ethylene glycol)-phospholipid for enhanced dispersion in water.

Cation⊗3π: cooperative interaction of a cation and three benzenes with an anomalous order in binding energy.

Cation-π or cation-π-π interaction between one cation and one or two structures bearing rich π-electrons (such as benzene, aromatic rings, graphene, and carbon nanotubes) plays a ubiquitous role in various areas. Here, we analyzed a new type interaction, cation⊗3π, whereby one cation simultaneously binds with three separate π-electron-rich structures. Surprisingly, we found an anomalous increase in the order of the one-benzene binding strength of the cation⊗3π interaction, with K(+) > Na(+) > Li(+).

Nanogold-assisted multi-round polymerase chain reaction (PCR).

We have previously demonstrated that nanogold effectively enhances the specificity and yield of error-prone two-round polymerase chain reaction (PCR). Here we reported that, with the assistance of nanogold, we could perform multi-round PCR. In the presence of appropriate amount of 10 nm nanogold, we could obtain the target product even after six rounds of PCR, as manifested by a single bright band in gel electrophoresis (1% agarose).

Nano-manipulation of single DNA molecules based on atomic force microscopy.

Nano-manipulation of single atoms and molecules is a critical technique in nanoscience and nanotechnology. This paper will focus on the recent development of the manipulation of single DNA molecules based on atomic force microscopy (AFM) in our laboratory. Precise manipulation has been realized including varied manipulating modes such as "cutting", "pushing", "folding", "kneading", "picking up", "dipping", etc.