The molecular organization of the human neocortex has been historically studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally-defined spatial domains that move beyond classic cytoarchitecture. Here we used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex (DLPFC). Integration with paired single nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we map the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains. Finally, we provide resources for the scientific community to explore these integrated spatial and single cell datasets at research.libd.org/spatialDLPFC/.

Purpose Children with a history of prematurity often have poorly developed foveae but when during development foveal differences arise. We hypothesize that the course of foveal development is altered from the time of preterm birth. Methods Eyes of 102 preterm infants undergoing retinopathy of prematurity screening examinations in the STudy of Eye imaging in Premature infantS (BabySTEPS) (NCT02887157) were serially imaged between 30 and 42 weeks postmenstrual age (PMA) using handheld optical coherence tomography systems. Total retinal thickness, inner retinal layer (IRL) thickness, and outer retinal layer (ORL) thickness were measured at the foveal center and parafovea. Foveal put depth, IRL thickness, and ORL thickness were compared between infants born at different gestational ages using mixed effects models. Results Foveal pit depth and IRL thickness were inversely related to gestational age; on average, the most premature infants had the thickest IRL and shallowest pits at all PMAs. Differences were evident by 30 weeks PMA and persisted through 42 weeks PMA. The foveal pits of the most premature infants did not progressively deepen, and the IRLs did not continue to thin with increasing chronological age. Conclusions Foveation in extremely preterm infants is arrested from the earliest observed ages and fails to progress through term equivalent age. The developmental displacement of the IRL from the foveal center into the parafovea does not occur normally after preterm birth. These observations suggest that foveal hypoplasia seen in children with history of prematurity is due to disturbances in foveal development that manifest within weeks of birth.

The lateral septum (LS), a GABAergic structure located in the basal forebrain, is implicated in social behavior, learning and memory. We previously demonstrated that expression of tropomyosin kinase receptor B (TrkB) in LS neurons is required for social novelty recognition. To better understand molecular mechanisms by which TrkB signaling controls behavior, we locally knocked down TrkB in LS and used bulk RNA-sequencing to identify changes in gene expression downstream of TrkB. TrkB knockdown induces upregulation of genes associated with inflammation and immune responses, and downregulation of genes associated with synaptic signaling and plasticity. Next, we generated one of the first atlases of molecular profiles for LS cell types using single nucleus RNA-sequencing (snRNA-seq). We identified markers for the septum broadly, and the LS specifically, as well as for all neuronal cell types. We then investigated whether the differentially expressed genes (DEGs) induced by TrkB knockdown map to specific LS cell types. Enrichment testing identified that downregulated DEGs are broadly expressed across neuronal clusters. Enrichment analyses of these DEGs demonstrated that downregulated genes are uniquely expressed in the LS, and associated with either synaptic plasticity or neurodevelopmental disorders. Upregulated genes are enriched in LS microglia, associated with immune response and inflammation, and linked to both neurodegenerative disease and neuropsychiatric disorders. In addition, many of these genes are implicated in regulating social behaviors. In summary, the findings implicate TrkB signaling in the LS as a critical regulator of gene networks associated with psychiatric disorders that display social deficits, including schizophrenia and autism, and with neurodegenerative diseases, including Alzheimer's.

MotivationRecent advances in spatially-resolved transcriptomics technologies such as 10x Genomics Visium platform have enabled the generation of transcriptome-wide spatial expression maps within intact tissue. However, steps for processing the high-resolution histology images, extracting relevant features from the images, and integrating them with the gene expression data remain unresolved.ResultsWe describe VistoSeg, a MATLAB pipeline to process, analyze, and interactively visualize the high-resolution images from the 10x Genomics Visium platform. The output from VistoSeg can then be integrated with the spatial-molecular information in downstream analyses using any programming language, such as R or Python.AvailabilityVistoSeg is available at https://github.com/LieberInstitute/VistoSeg (DOI: 10.5281/zenodo.5156783) with a tutorial at http://research.libd.org/VistoSegSupplementary informationSupplementary data are available at Bioinformatics online.

Magnetospirillum magneticum (AMB-1) are a species of magnetotactic bacteria (MTB) that are capable of orienting along the earth’s magnetic field lines through their organelles called magnetosomes. Many studies have shown that certain engineered bacteria can infect the tumor cells, resulting in a controlled death of a tumor. This work deals with a technique utilizing AMB-1 along a predefined path through magnetotaxis, which can pave a way for selective doping as well as isolation of the tumor cells from a group of healthy cells through a magnetic invasive assay. For such a control, a tiny mesh of vertical electrical coils each having a diameter of ∼3 mm is fabricated, which establishes the path for the bacteria to move along the magnetic field lines. The molecular dynamics (MD) simulations at the interface of the bacterial cell surface proteins (MSP-1 and flagellin) and Chinese hamster ovary (CHO) cell surface containing cytoplasmic and extracellular proteins (BSG, B2M, SDC1, AIMP1, and FOS) are shown to establish an association between the AMB-1 and the host CHO cells. It is found that the CHO protein structure is compromised, which disables the activation of its defense function, allowing the bacteria to interact and survive. The experimental demonstration involves the CHO cells’ interaction with the AMB-1 and isolation of selected CHO cells. It is found that AMB-1-integrated CHO cells successfully moved along the magnetic field lines generated by the coils. Statistical analysis performed for the assay showed that AMB-1 cells were found to be viable after co-incubating with CHO cells, and the number of viable cells post co-incubation over a period of 24 h showed a slight decrease in both cell population. Overall, 51% of AMB-1 cells and 67% of CHO cells were found viable 24 h post co-incubation. Scanning electron microscopy (SEM) along with energy-dispersive X-ray spectroscopy (EDAX) analysis revealed AMB-1/CHO cell morphology, the potential interaction between them, and the presence of magnetosomes with trace amounts of iron in the AMB-1-interacted CHO cells, confirming the successful AMB-1 integration.