Single-cell genomics and regulatory networks for 388 human brains.

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multiomics datasets into a resource comprising >2.8 million nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550,000 cell type-specific regulatory elements and >1.4 million single-cell expression quantitative trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.

Single-cell genomics and regulatory networks for 388 human brains.

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.

Effects of wollastonite and phosphate treatments on cadmium bioaccessibility in pak choi (Brassica rapa L. ssp. chinensis) grown in contaminated soils.

Cadmium (Cd) contamination of soil can strongly impact human health through the food chain due to uptake by crop plants. Inorganic immobilizing agents such as silicates and phosphates have been shown to effectively reduce Cd transfer from the soil to cereal crops. However, the effects of such agents on total Cd and its bioaccessibility in leafy vegetables are not yet known. Pak choi (Brassica rapa L. ssp. chinensis) was here selected as a representative leafy vegetable to be tested in pots to reveal the effects of silicate-phosphate amendments on soil Cd chemical fractions, total plant Cd levels, and plant bioaccessibility. The collected Cd contaminated soil was mixed with control soil at 1:0, 1:1, 1:4, 0:1 with a view to Cd high/moderate/mild/control soil samples. Three heavy metal-immobilizing agents: wollastonite (W), potassium tripolyphosphate (KTPP), and sodium hexametaphosphate (SHMP) were added to the soil in order to get four different treatment groups, i.e., control (CK), application of wollastonite alone (W), wollastonite co-applied with KTPP (WKTPP), application of wollastonite co-applied with SHMP (WSHMP) for remediation of soils with different levels of Cd contamination. All three treatments increased the effective bio-Cd concentration in the soils with varying levels of contamination, except for W under moderate and heavy Cd contamination. The total Cd concentration in pak choi plants grown in mildly Cd-contaminated soil was elevated by 86.2% after WKTPP treatment compared to the control treatment could function as a phytoremediation aid for mildly Cd-contaminated soil. Using an in vitro digestion method (physiologically based extraction test) combined with transmission electron microscopy, silicate and phosphorus agents were found to reduce the bioaccessibility of Cd in pak choi by up to 66.13% with WSHMP treatment. Application of silicate alone reduced soil bio-Cd concentration through the formation of insoluble complexes and silanol groups with Cd, but the addition of phosphate may have facilitated Cd translocation into pak choi by first co-precipitating with Ca in wollastonite while simultaneously altering soil pH. Meanwhile, wollastonite and phosphate treatments may cause Cd to be firmly enclosed in the cell wall in an insoluble form, reducing its translocation to edible parts and decreasing the bioaccessibility of Cd in pak choi. This study contributes to the mitigation of Cd bioaccessibility in pak choi by reducing soil Cd concentration through in situ remediation and will help us to extend the effects of wollastonite and phosphate on Cd bioaccessibility to other common vegetables. Therefore, this study thus reveals effective strategies for the remediation of soil Cd and the reduction of Cd bioaccessibility in crops based on two indicators: total Cd and Cd bioaccessibility. Our findings contribute to the development of methods for safer cultivation of commonly consumed leafy vegetables and for soil remediation.

Partitioning surface wave propagation on reconfigurable porous plane.

This paper introduces a novel reconfigurable technique for partitioning the propagation of surface waves by utilizing a T-shaped structure and pathways established through the introduction of fluid metal or metal pins into evenly spaced cylindrical cavities within a porous surface wave platform. Notably, the co-printing of metal and dielectric materials via 3D printing is employed, resulting in an expedited fabrication process. Extensive 3D electromagnetic simulations and experimental investigations validate the proposed approach's efficacy in achieving surface wave division while minimizing interference. The study encompasses an exploration of diverse power distribution ratios achievable within the distributed surface waves. Critical physical parameters of the T-junction are comprehensively examined, including partition depth, junction geometry, output port symmetry, and asymmetry. Additionally, the research delves into the frequency-dependent behaviours of asymmetric T-junctions and pathways. These findings establish the groundwork for adaptable architectures, facilitating concurrent communication among multiple devices within a unified surface wave communication network. This innovation holds potential to enhance various applications through improved communication capabilities.

Massively parallel knock-in engineering of human T cells.

The efficiency of targeted knock-in for cell therapeutic applications is generally low, and the scale is limited. In this study, we developed CLASH, a system that enables high-efficiency, high-throughput knock-in engineering. In CLASH, Cas12a/Cpf1 mRNA combined with pooled adeno-associated viruses mediate simultaneous gene editing and precise transgene knock-in using massively parallel homology-directed repair, thereby producing a pool of stably integrated mutant variants each with targeted gene editing. We applied this technology in primary human T cells and performed time-coursed CLASH experiments in blood cancer and solid tumor models using CD3, CD8 and CD4 T cells, enabling pooled generation and unbiased selection of favorable CAR-T variants. Emerging from CLASH experiments, a unique CRISPR RNA (crRNA) generates an exon3 skip mutant of PRDM1 in CAR-Ts, which leads to increased proliferation, stem-like properties, central memory and longevity in these cells, resulting in higher efficacy in vivo across multiple cancer models, including a solid tumor model. The versatility of CLASH makes it broadly applicable to diverse cellular and therapeutic engineering applications.

CRISPR-GEMM Pooled Mutagenic Screening Identifies KMT2D as a Major Modulator of Immune Checkpoint Blockade.

Immune checkpoint blockade (ICB) has shown remarkable clinical efficacy in several cancer types. However, only a fraction of patients will respond to ICB. Here, we performed pooled mutagenic screening with CRISPR-mediated genetically engineered mouse models (CRISPR-GEMM) in ICB settings, and identified KMT2D as a major modulator of ICB response across multiple cancer types. KMT2D encodes a histone H3K4 methyltransferase and is among the most frequently mutated genes in patients with cancer. Kmt2d loss led to increased DNA damage and mutation burden, chromatin remodeling, intron retention, and activation of transposable elements. In addition, Kmt2d-mutant cells exhibited increased protein turnover and IFNγ-stimulated antigen presentation. In turn, Kmt2d-mutant tumors in both mouse and human were characterized by increased immune infiltration. These data demonstrate that Kmt2d deficiency sensitizes tumors to ICB by augmenting tumor immunogenicity, and also highlight the power of CRISPR-GEMMs for interrogating complex molecular landscapes in immunotherapeutic contexts that preserve the native tumor microenvironment. SIGNIFICANCE: ICB is ineffective in the majority of patients. Through direct in vivo CRISPR mutagenesis screening in GEMMs of cancer, we find Kmt2d deficiency sensitizes tumors to ICB. Considering the prevalence of KMT2D mutations, this finding potentially has broad implications for patient stratification and clinical decision-making.This article is highlighted in the In This Issue feature, p. 1775.

[Mapping and genetic effect analysis of quantitative trait loci related to body length in mirror carp (Cyprinus carpio L.)].

A group of F2 hybrids of mirror carp including 68 individuals was used to construct a linkage map using JoinMap4.0 software. Of 560 markers genotyped, 507 markers (143 SSR markers, 33 EST-SSR markers, and 321 SNP markers) were assigned to the map, which comprised of 62 linkage groups. Quantitative traits loci (QTLs) associated with body length were identified by interval mapping of the software MapQTL 5.0. A linkage group wide permutation test (1 000 replicates) determined the significance of the maximum LOD value over the various intervals analyzed for each linkage group. Twelve QTLs were identified for body length on the linkage groups of BL-1-1 (SNP0137-SNP1481), BL-4-1 (SNP0092-HLJ797), BL-5-1 (SNP1268-HLJ423), BL-7-1 (HLJ870-SNP0702), BL-12-1 (SNP0922-HLJ639), BL-16-1 (HLJE351-SNP0674), BL-25-1 (SNP0394-SNP0862), BL-35-1 (HLJ668-SNP0832), BL-43-1 (SNP0389-SNP1425), BL-47-1 (HLJ057-HLJ1113), BL-47-2 (HLJ1439-HLJ14180), which explained 13.8% to 64.9% of the total variation of body length. Eight major QTLs explained over 20% of the phenotypic variation, which were major QTLs associated with the body length of mirror carp.