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.

Molecular cascades and cell type-specific signatures in ASD revealed by single-cell genomics.

Genomic profiling in postmortem brain from autistic individuals has consistently revealed convergent molecular changes. What drives these changes and how they relate to genetic susceptibility in this complex condition are not well understood. We performed deep single-nucleus RNA sequencing (snRNA-seq) to examine cell composition and transcriptomics, identifying dysregulation of cell type-specific gene regulatory networks (GRNs) in autism spectrum disorder (ASD), which we corroborated using single-nucleus assay for transposase-accessible chromatin with sequencing (snATAC-seq) and spatial transcriptomics. Transcriptomic changes were primarily cell type specific, involving multiple cell types, most prominently interhemispheric and callosal-projecting neurons, interneurons within superficial laminae, and distinct glial reactive states involving oligodendrocytes, microglia, and astrocytes. Autism-associated GRN drivers and their targets were enriched in rare and common genetic risk variants, connecting autism genetic susceptibility and cellular and circuit alterations in the human brain.

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.

Molecular cascades and cell-type specific signatures in ASD revealed by single cell genomics.

Understanding how genetic variation exerts its effects on the human brain in health and disease has been greatly informed by functional genomic characterization. Studies over the last decade have demonstrated robust evidence of convergent transcriptional and epigenetic profiles in post-mortem cerebral cortex from individuals with Autism Spectrum Disorder (ASD). Here, we perform deep single nuclear (sn) RNAseq to elucidate changes in cell composition, cellular transcriptomes and putative candidate drivers associated with ASD, which we corroborate using snATAC-seq and spatial profiling. We find changes in cell state composition representing transitions from homeostatic to reactive profiles in microglia and astrocytes, a pattern extending to oligodendrocytes and blood brain barrier cells. We identify profound changes in differential expression involving thousands of genes across neuronal and glial subtypes, of which a substantial portion can be accounted for by specific transcription factor networks that are significantly enriched in common and rare genetic risk for ASD. These data, which are available as part of the PsychENCODE consortium, provide robust causal anchors and resultant molecular phenotypes for understanding ASD changes in human brain.

Construction of azaspirocyclic skeletons mediated by the carbonyl of the Weinreb amide: formal total synthesis of (±)-cephalotaxine.

A facile Stevens rearrangement of the Weinreb amide and the subsequent key steps mediated by the carbonyl of the Weinreb amide led to the construction of azaspirocyclic skeletons of some typical alkaloids. And the formal total synthesis of (±)-cephalotaxine was completed via a shorter synthetic route by this efficient method. Further studies on the development and asymmetric synthesis application of this strategy are underway.

Phylogenetic diversity of nitrogen-fixing bacteria and the nifH gene from mangrove rhizosphere soil.

Nine types of nitrogen-fixing bacterial strains were isolated from 3 rhizosphere soil samples taken from mangrove plants in the Dongzhaigang National Mangrove Nature Reserve of China. Most isolates belonged to Gammaproteobacteria Pseudomonas, showing that these environments constituted favorable niches for such abundant nitrogen-fixing bacteria. New members of the diazotrophs were also found. Using a soil DNA extraction and PCR-cloning-sequencing approach, 135 clones were analyzed by restriction fragment length polymorphism (RFLP) analysis, and 27 unique nifH sequence phylotypes were identified, most of which were closely related to sequences from uncultured bacteria. The diversity of nitrogen-fixing bacteria was assessed by constructing nifH phylogenetic trees from sequences of all isolates and clones in this work, together with related nifH sequences from other mangrove ecosystems in GenBank. The nifH diversity varied among soil samples, with distinct biogeochemical properties within a mangrove ecosystem. When comparing different mangrove ecosystems, the nifH gene sequences from a specific site tended to cluster as individual groups. The results provided interesting data and novel information on our understanding of diazotroph community diversity in the mangrove ecosystems.

[An improved surgical strategy and treatment outcome of dorsal wrist ganglion].

OBJECTIVE: To investigate the clinical outcome of treating dorsal wrist ganglion with an improved surgical strategy by excising the ganglion completely along their stalk and repairing the dorsal carpal ligaments under brachial anesthesia. METHODS: From March 2005 to January 2007, 34 patients with dorsal wrist ganglion were treated and studied retrospectively. There were 14 males and 20 females, aged 25-65 years (43 years on average). The left sides were involved in 22 cases and right sides in 12 cases. Thirteen cases of relapse received excision for 1 to 4 times under local anesthesia, with a mean period of 17 months (14 days to 7 years) from excision to recurrence. Twenty-one patients were first attack cases with a mean period of 11 months (15 days to 8 years) from diagnosis to excision. The size of the ganglion ranged from 1.5 cm x 1.2 cm to 4.5 cm x 4.0 cm. Now, each surgical process was performed under brachial anesthesia, and a pneumathode tourniquet was used. In 6 patients, the stalks of ganglion did not invade the carpal ligaments, and ganglion was removed completely without immobilization after operation. In 28 patients, the stalks of ganglion invaded the carpal ligaments, ganglion was excised completely along its stalk to the dorsal carpal structure; the ligaments were sutured directly in 16 cases and were repaired with adjacent tissue such as the wall of sheathing canal of extensor tendon in 12 cases. The wrists were immobilised for 3 weeks. RESULTS: Primary wound healing was achieved in all incisions. All patients were followed up for 26-36 months with an average of 31.5 months. Only 2 cases (5.9%) recurred. The range of motion of the wrist remained normal and the symptom of the dorsal wrist was relieved slightly. Patients' satisfaction score ranged from 60 to 100, with an average of 83.8. CONCLUSION: The ganglion should be excised completely together with defect repair of dorsal carpal ligament under brachial anesthesia and the wrist immobilised for 3 weeks, the recurrence rate will be reduced greatly.