Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasite Trypanosoma brucei and induces profound reactivity of glial cells and neuroinflammation when the parasites colonise the central nervous system. However, the transcriptional and functional responses of the brain to chronic T. brucei infection remain poorly understood. By integrating single cell and spatial transcriptomics of the mouse brain, we identify that glial responses triggered by infection are readily detected in the proximity to the circumventricular organs, including the lateral and 3rd ventricle. This coincides with the spatial localisation of both slender and stumpy forms of T. brucei. Furthermore, in silico predictions and functional validations led us to identify a previously unknown crosstalk between homeostatic microglia and Cd138+ plasma cells mediated by IL-10 and B cell activating factor (BAFF) signalling. This study provides important insights and resources to improve understanding of the molecular and cellular responses in the brain during infection with African trypanosomes. 

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Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection

Spatial transcriptomics technologies are used to profile transcriptomes while preserving spatial information, which enables high-resolution characterization of transcriptional patterns and reconstruction of tissue architecture. Due to the existence of low-resolution spots in recent spatial transcriptomics technologies, uncovering cellular heterogeneity is crucial for disentangling the spatial patterns of cell types, and many related methods have been proposed. Here, we benchmark 18 existing methods resolving a cellular deconvolution task with 50 real-world and simulated datasets by evaluating the accuracy, robustness, and usability of the methods. We compare these methods comprehensively using different metrics, resolutions, spatial transcriptomics technologies, spot numbers, and gene numbers. In terms of performance, CARD, Cell2location, and Tangram are the best methods for conducting the cellular deconvolution task. To refine our comparative results, we provide decision-tree-style guidelines and recommendations for method selection and their additional features, which will help users easily choose the best method for fulfilling their concerns. 

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A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

Age-associated changes in DNA methylation have been widely established and characterized in mammals but not yet extended to other species. We present clear evidence that the aquatic vertebrate species Xenopus tropicalis displays clear patterns of age-associated changes in DNA methylation. This observation allows us to leverage the unique resources available for Xenopus to study how DNA methylation relates to other hallmarks of aging. We have generated whole genome bisulfite sequencing (WGBS) profiles in nine samples representing young, mature and old adults and characterize the gene- and chromosome-scale changes. Moreover, we selected a few thousands CpG sites to expand the findings in a larger cohort of individuals through targeted DNA methylation analysis to produce a cost effective epigenetic clock assay.

Age-associated DNA methylation changes in Xenopus frogs

Understanding the aging hypothalamus, one cell at a time

Thyroid hormone and its receptor TRα1 play an important role in brain development. Several animal models have been used to investigate this function, including mice heterozygous for the TRα1R384C mutation, which confers receptor-mediated hypothyroidism. These mice display abnormalities in several autonomic functions, which was partially attributed to a developmental defect in hypothalamic parvalbumin neurons. However, whether other cell types in the hypothalamus are similarly affected remains unknown. Here, we used single-nucleus RNA sequencing to obtain an unbiased view on the importance of TRα1 for hypothalamic development and cellular diversity. Our data show that defective TRα1 signaling has surprisingly little effect on the development of hypothalamic neuronal populations, but it heavily affects hypothalamic oligodendrocytes. Using selective reactivation of the mutant TRα1 during specific developmental periods, we find that early postnatal thyroid hormone action seems to be crucial for proper hypothalamic oligodendrocyte maturation. Taken together, our findings underline the well-known importance of postnatal thyroid health for brain development and provide an unbiased roadmap for the identification of cellular targets of TRα1 action in mouse hypothalamic development.

Single-cell RNA-based phenotyping reveals a pivotal role of thyroid hormone receptor alpha for hypothalamic development.

Abstract Alterations in metabolism, sleep patterns, body composition and hormone status are all key features of aging. While the hypothalamus is a well-conserved brain region that controls these homeostatic and survival-related behaviors, little is known about the intrinsic features of hypothalamic aging. Here, we perform single-nuclei RNA sequencing of 40,064 hypothalamic nuclei from young and aged female mice. We identify cell type-specific signatures of aging in neuronal subtypes as well as astrocytes and microglia. We uncover changes in cell types critical for metabolic regulation and body composition and in an area of the hypothalamus linked to cognition. Our analysis also reveals an unexpected female-specific feature of hypothalamic aging: the master regulator of X inactivation, Xist , is elevated with age, particularly in hypothalamic neurons. Moreover, using machine learning, we show that levels of X chromosome genes and Xist itself, can accurately predict cellular age. This study identifies critical cell-specific changes of the aging hypothalamus in mammals and uncovers a potential marker of neuronal aging in females. 

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Sarah Packer

Papers

Single-cell analysis of the aging female mouse hypothalamus