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Objectives: The caecum bridges the small and large intestine and plays a front‐line role in discriminating gastrointestinal antigens. Although dysregulated in acute and chronic conditions, the tissue is often overlooked immunologically. Methods: To address this issue, we applied single‐cell transcriptomic‐V(D)J sequencing to FACS‐isolated CD45+ caecal patch/lamina propria leukocytes from a healthy (5‐year‐old) female rhesus macaque ex vivo and coupled these data to VDJ deep sequencing reads from haematopoietic tissues. Results: We found caecal NK cells and ILC3s to co‐exist with a spectrum of effector T cells partially derived from SOX4+ recent thymic emigrants. Tolerogenic Vγ8Vδ1‐T cells, plastic CD4+ T helper cells and GZMK+EOMES+ and TMIGD2+ tissue‐resident memory CD8+ T cells were present and differed metabolically. An IL13+GATA3+ Th2 subset expressing eicosanoid pathway enzymes was accompanied by IL1RL1+GATA3+ regulatory T cells and a minor proportion of IgE+ plasma cells (PCs), illustrating tightly regulated type 2 immunity devoid of ILC2s. In terms of B lymphocyte lineages, caecal patch antigen‐presenting memory B cells sat alongside germinal centre cells undergoing somatic hypermutation and differentiation into IGF1+ PCs. Prototypic gene expression signatures decreased across PC clusters, and notably, expanded IgA clonotypes could be traced in VDJ deep sequencing reads from additional compartments, including the bone marrow, supporting that these cells contribute a steady stream of systemic antibodies. Conclusions: The data advance our understanding of caecal immunological function, revealing processes involved in barrier maintenance and molecular networks relevant to disease. [ABSTRACT FROM AUTHOR]

One promising goal for utilizing the molecular information circulating in biofluids is the discovery of clinically useful biomarkers. Extracellular RNAs (exRNAs) are one of the most diverse classes of molecular cargo, easily assayed by sequencing and with expressions that rapidly change in response to subject status. Despite diverse exRNA cargo, most evaluations from biofluids have focused on small RNA sequencing and analysis, specifically on microRNAs (miRNAs). Another goal of characterizing circulating molecular information, is to correlate expression to injuries associated with specific tissues of origin. Biomarker candidates are often described as being specific, enriched in a particular tissue or associated with a disease process. Likewise, miRNA data is often reported to be specific, enriched for a tissue, without rigorous testing to support the claim. Here we provide a tissue atlas of small RNAs from 30 different tissues and three different blood cell types. We analyzed the tissues for enrichment of small RNA sequences and assessed their expression in biofluids: plasma, cerebrospinal fluid, urine, and saliva. We employed published data sets representing physiological (resting vs. acute exercise) and pathologic states (early- vs. late-stage liver fibrosis, and differential subtypes of stroke) to determine differential tissue-enriched small RNAs. We also developed an online tool that provides information about exRNA sequences found in different biofluids and tissues. The data can be used to better understand the various types of small RNA sequences in different tissues as well as their potential release into biofluids, which should help in the validation or design of biomarker studies.

Summary: Sphingolipids (SPs) have both a structural role in the cell membranes and a signaling function that regulates many cellular processes. The enormous structural diversity and low abundance of many SPs pose a challenge for their identification and quantification. Recent advances in lipidomics, in particular liquid chromatography (LC) coupled with mass spectrometry (MS), provide methods to detect and quantify many low-abundant SP species reliably. Here we use LC-MS to compile a “murine sphingolipid atlas,” containing the qualitative and quantitative distribution of 114 SPs in 21 tissues of a widely utilized wild-type laboratory mouse strain (C57BL/6). We report tissue-specific SP fingerprints, as well as sex-specific differences in the same tissue. This is a comprehensive, quantitative sphingolipidomic map of mammalian tissues collected in a systematic fashion. It will complement other tissue compendia for interrogation into the role of SP in mammalian health and disease.

PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues.

One promising goal for utilizing the molecular information circulating in biofluids is the discovery of clinically useful biomarkers. Extracellular RNAs (exRNAs) are one of the most diverse classes of molecular cargo, easily assayed by sequencing and with expressions that rapidly change in response to subject status. Despite diverse exRNA cargo, most evaluations from biofluids have focused on small RNA sequencing and analysis, specifically on microRNAs (miRNAs). Another goal of characterizing circulating molecular information, is to correlate expression to injuries associated with specific tissues of origin. Biomarker candidates are often described as being specific, enriched in a particular tissue or associated with a disease process. Likewise, miRNA data is often reported to be specific, enriched for a tissue, without rigorous testing to support the claim. Here we provide a tissue atlas of small RNAs from 30 different tissues and three different blood cell types. We analyzed the tissues for enrichment of small RNA sequences and assessed their expression in biofluids: plasma, cerebrospinal fluid, urine, and saliva. We employed published data sets representing physiological (resting vs. acute exercise) and pathologic states (early- vs. late-stage liver fibrosis, and differential subtypes of stroke) to determine differential tissue-enriched small RNAs. We also developed an online tool that provides information about exRNA sequences found in different biofluids and tissues. The data can be used to better understand the various types of small RNA sequences in different tissues as well as their potential release into biofluids, which should help in the validation or design of biomarker studies., Competing Interests: KV and SD are members of the scientific advisory board at Dyrnamix. Their involvement in this company had no bearing on the work performed in this manuscript. KV is on the scientific advisory board of HTG. Her involvement has no bearing on this work. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Alsop, Meechoovet, Kitchen, Sweeney, Beach, Serrano, Hutchins, Ghiran, Reiman, Syring, Hsieh, Courtright-Lim, Valkov, Whitsett, Rakela, Pockros, Rozowsky, Gallego, Huentelman, Shah, Nakaji, Kalani, Laurent, Das and Van Keuren-Jensen.)

Sphingolipids (SPs) have both a structural role in the cell membranes and a signaling function that regulates many cellular processes. The enormous structural diversity and low abundance of many SPs pose a challenge for their identification and quantification. Recent advances in lipidomics, in particular liquid chromatography (LC) coupled with mass spectrometry (MS), provide methods to detect and quantify many low-abundant SP species reliably. Here we use LC-MS to compile a "murine sphingolipid atlas," containing the qualitative and quantitative distribution of 114 SPs in 21 tissues of a widely utilized wild-type laboratory mouse strain (C57BL/6). We report tissue-specific SP fingerprints, as well as sex-specific differences in the same tissue. This is a comprehensive, quantitative sphingolipidomic map of mammalian tissues collected in a systematic fashion. It will complement other tissue compendia for interrogation into the role of SP in mammalian health and disease. [Display omitted] • Sphingolipids atlas of 21 tissues from C57BL/6 mice • Quantitative differences of sphingolipids across tissues • Sex-specific differences in the sphingolipidome of 21 mouse tissues • Effect of high-fat diet on the sphingolipidome Sphingolipids are involved in numerous cellular processes, but a systematic and comprehensive map of their tissue distribution is missing. Using targeted lipidomics, Muralidharan et al. provide quantitative and qualitative profiles of 114 sphingolipid species across 21 murine tissues, highlighting their variation as a function of sex and diet. [ABSTRACT FROM AUTHOR]

Micro-computed tomography (μCT) and contrast-enhanced μCT are important tools for preclinical analysis of bone and articular cartilage (AC). Quantitative data from these modalities is highly dependent on the accuracy of tissue segmentations, which are often obtained via time-consuming manual contouring and are prone to inter- and intra-observer variability. Automated segmentation strategies could mitigate these issues, but few such approaches have been described in the context of μCT. Here, we validated a fully-automated strategy for bone and AC segmentation based on registration of an average tissue atlas. Femora from healthy and arthritic rats underwent μCT scanning, and epiphyseal trabecular bone and AC volumes were manually contoured by an expert. Average tissue atlases composed of 1, 3, 5, 10 and 20 pre-contoured training images (n = 10 atlases/group) were generated using iterative shape averaging and registered onto unknown images via affine and non-rigid registration. Atlas-based and expert-defined volumes for bone and AC were compared in terms of shape-based similarity metrics, as well as morphometric and densitometric parameters. Our results demonstrate that atlas-based registrations were capable of highly accurate and consistent segmentation. Atlases built from as few as 3 training images had no incidence of mal-registration and exhibited improved incidence of accurate registration, and higher sensitivity and specificity compared to atlases built from only one training image. Atlas-based segmentation of bone and AC from μCT images is a robust and accurate alternative to manual tissue segmentation, enabling faster, more consistent segmentation of pre-clinical datasets. Unlabelled Image • Atlas-based segmentation effectively delineates tissue boundaries on preclinical microCT. • Cartilage, bone tissues were accurately segmented from microCT images of rat femora. • Average atlases built from multiple samples were more robust than 1-sample atlases. • Three-to-five training samples were sufficient to produce a robust average atlas. [ABSTRACT FROM AUTHOR]

PKA (protein lysine acetylation) is a key post-translational modification involved in the regulation of various biological processes in rice. So far, rice acetylome data is very limited due to the highly-dynamic pattern of protein expression and PKA modification. In this study, we performed a comprehensive quantitative acetylome profile on four typical rice tissues, i.e., the callus, root, leaf, and panicle, by using a mass spectrometry (MS)-based, label-free approach. The identification of 1536 acetylsites on 1454 acetylpeptides from 890 acetylproteins represented one of the largest acetylome datasets on rice. A total of 1445 peptides on 887 proteins were differentially acetylated, and are extensively involved in protein translation, chloroplast development, and photosynthesis, flowering and pollen fertility, and root meristem activity, indicating the important roles of PKA in rice tissue development and functions. The current study provides an overall view of the acetylation events in rice tissues, as well as clues to reveal the function of PKA proteins in physiologically-relevant tissues. [ABSTRACT FROM AUTHOR]