scRNA-seq anda spatial transcriptomics

To systematically characterize the loss of tissue integrity and organ dysfunction resulting from aging, we produced an in-depth spatial transcriptomic profile of nine tissues in male mice during aging. We showed that senescence-sensitive spots (SSSs) colocalized with elevated entropy in organizational structure and that the aggregation of immunoglobulin-expressing cells is a characteristic feature of the microenvironment surrounding SSSs. Immunoglobulin G (IgG) accumulated across the aged tissues in both male and female mice, and a similar phenomenon was observed in human tissues, suggesting the potential of the abnormal elevation of immunoglobulins as an evolutionarily conserved feature in aging. Furthermore, we observed that IgG could induce a pro-senescent state in macrophages and microglia, thereby exacerbating tissue aging, and that targeted reduction of IgG mitigated aging across various tissues in male mice. This study provides a high-resolution spatial depiction of aging and indicates the pivotal role of immunoglobulin-associated senescence during the aging process.

Recent discoveries about the molecular heterogeneity of the cerebellar cortex suggest the existence of functionally divergent subclasses of anatomically defined cell types. Using spatial transcriptome and single-nucleus RNA-seq analysis, we mapped 3D transcriptomic atlases of the whole cerebellum of mice, marmosets, and macaques at the single-cell resolution. Comparative analysis revealed specific cell types, cell localizations, and intra-cerebellum molecular heterogeneity across species. A comprehensive database generated from this study will expand the acknowledgment of the mammalian cerebellum.

" The molecular and cellular mechanisms underlying the function of the cochlear nucleus (CN) remain to be fully elucidated. Using single-nucleus RNA sequencing and single-cell spatial transcriptome analyses, we identified transcriptome-defined cell types, as well as their spatial distribution and marker genes. These data also allowed us to acquire a new definition of CN subregions. By comparing transcriptomic profiles between normal mice and mutant mice with congenital hearing loss due to hair cell malfunction, we further identified glutamatergic Spp1+-bushy cell as a primary cell type exhibiting hearing loss-induced alteration in gene expression. Among highly affected genes in the bushy cell, we found that deletion of a developmentally regulated osteopontin-encoding gene Spp1 affected CN processing of auditory signals. Together, our study provides the most comprehensive molecular and cellular atlas of CN to date and identifies critical hearing loss-related cell types and specific genes that may serve as potential therapeutic targets. "

The higher-order cognitive functions of the human cortex rely on complex cellular structures, with diversity and spatial organization critical for specific functions. However, the molecular features and precise spatial organization of neural cells within the human cortex remain incompletely understood. Subcellular-level spatial transcriptomic sequencing and snRNA-seq offer a unique opportunity to explore and characterize neural cell organization across different cortical regions. Here, we mapped 14 human cortical regions, leading to a single-cell atlas comprising transcriptomic data from 1,121,772 nuclei and spatial profiles from 1,888,306 cells. The atlas reveals distinct expression patterns and spatial arrangements of neural cell types. Glutamatergic neurons show precise laminar patterns, with similar expression in adjacent areas. SST neurons fall into two transcriptional categories, corresponding to superficial and deep layer distributions. The atlas, integrated with functional networks, highlights correlations between neural cell types and cortical functions, uncovering cell-cell interactions and ligand-receptor patterns with regional differences in neuron-glia communication. It also deciphers transcriptomic differences and cellular composition in layer 4 and the stable subplate (layer 6b) across regions. Our findings offer insights into the cellular foundations of complex and intelligent regions within the human cortex.

The evolution of amniotes introduced the emergence of intricate brain organization, particularly in the telencephalon, but its genoarchitectonic identity and evolutionary trajectory remain unclear. By constructing spatial transcriptomic atlases of the zebra finch and turtle telencephalon, we enable unparalleled comparisons among sauropsids (reptiles and birds), allowing us to decode the evolutionary origins of the complex DVR subregions in sauropsids. Notably, we elucidated the molecular mechanism by which the avian DVR and mammalian neocortex recruit the same effector genes via divergent transcription factors, underscoring their functional convergent evolution. Collectively, our data shed light on the nuanced evolutionary relationships within the telencephalon among amniotes, providing a new fundamental understanding of brain evolution.

Cholestatic injuries, characterized by regional damage around the periportal region, lack curative therapies and cause considerable mortality. In this study, we generated a high-definition spatiotemporal atlas during cholestatic injury and repair by Stereo-seq and single-cell transcriptomics. We uncovered that cholangiocytes function as a periportal hub (cholangio-hub) by integrating multiple signals with neighboring cells. Feedback between cholangiocytes and lipid-associated macrophages (LAM) was detected in the cholangio-hub, which is related to the differentiation of LAM, a recently identified subpopulation of macrophages crucial in tissue injury. Moreover, the cholangio-hub highly expressed TGFβ, which is associated with cholangiocyte conversion of liver progenitor-like cells during injury and dampened proliferation of periportal hepatocytes during recovery. Importantly, spatiotemporal analysis revealed a key inhibitory rheostat for hepatocyte proliferation. Our data provide a comprehensive resource for demarcating regional cholestatic injuries.

Although the hypothalamus plays a crucial role in the progression of metabolic diseases including obesity and diabetes, the underlying molecular remodeling remains unclear. Here we systematically compared the transcriptomic features of structured hypothalamus at single-cell resolution in obese and diabetic macaques. We found that the infundibular (INF) and the paraventricular nucleus (PVN) were the most susceptible regions to metabolic disruption with the PVN being more sensitive to diabetes. In the INF, obesity displayed reduced synaptic plasticity and energy sensing capability. By contrast, in diabetes there was interactive molecular reprogramming associated with an impaired tanycyte barrier, activated microglia and stimulation of neuronal inflammatory response. Results from Stereo-seq further demonstrate a unique spatial tropism of microglia towards parenchyma relative to the third ventricle. Our data provide an extensive reference resource of distinct molecular changes between obesity and diabetes in the primate hypothalamus, which may facilitate more precise and effective therapies for metabolic disorders.

Optimization and application of clustering algorithms in integrated analysis of multiomics dataset

Transitions between root and shoot identities are central to plant development and regeneration. Here, we identify a transitional cell (TC) state in Arabidopsis thaliana that bridges these identity switches during de novo shoot regeneration, with parallels suggested during embryogenesis. This TC state consists of two distinct populations: a shoot progenitor population and surrounding boundary cells that collaborate to form a functional shoot system. During a brief transitional phase, these cells exhibit overlapping root- and shoot-specific gene expression, orchestrated by antagonistic interactions between the homeotic factors ATML1 and WOX5. MYB31 is identified as a key regulator that shifts this balance toward shoot formation. By integrating single-nucleus RNA sequencing and spatial transcriptomics, we delineate the molecular signatures, spatial organization, and developmental trajectories of these populations. This study provides a conceptual framework for understanding root-to-shoot transitions and lays the groundwork for engineering plant regeneration, with applications in crop improvement and sustainable agriculture.