Evaluation of Commercially Available Glucagon Receptor Antibodies and Glucagon Receptor Expression

Glucagon is a key regulator of numerous metabolic functions including glucose, protein and lipid metabolism, and glucagon-based therapies are explored for diabetes, fatty liver disease and obesity. Insight into tissue and cell specific expression of the glucagon receptor (GCGR) is important to understand the biology of glucagon as well as to differentiate between direct and indirect actions of glucagon. However, it has been challenging to accurately localize the GCGR in tissue due to low expression levels and lack of specific methodologies. Immunohistochemistry has frequently been used for GCGR localization, but G-protein-coupled receptors (GPCRs) targeting antibodies are notoriously unreliable. In this study, we systematically evaluated all commercially available GCGR antibodies. Initially, twelve GCGR antibodies were evaluated using HEK293 cells transfected with mouse or human GCGR cDNA. Of the twelve antibodies tested, eleven showed positive staining of GCGR protein from both species. Human liver tissue was investigated using the same GCGR antibodies. Five antibodies failed to stain human liver biopsies (despite explicit claims to the contrary from the vendors). Immunohistochemical (IHC) staining demonstrated positive staining of liver tissue from glucagon receptor knockout (Gcgr-/-) mice and their wild-type littermates (Gcgr+/+) with only one out of the twelve available GCGR antibodies. Three antibodies were selected for further evaluation by western blotting and bands corresponding to the predicted size of the GCGR (62 kDa) were identified using two of these. Finally, a single antibody (no. 11) was selected for specific GCGR localization studies in various tissues. In mouse tissue the most intense immunostainings were found in lever, kidney, ileum, heart, and pancreas. Western blotting, performed on liver tissue from Gcgr+/+ and Gcgr-/- mice, confirmed the specificity of antibody no. 11, detecting a band at high intensity in material from Gcgr+/+and no bands in liver tissue from Gcgr-/-mice. Staining of human kidney tissue, with antibody no. 11, showed GCGR localization to the distal tubules. Autoradiography was used as an antibody-independent approach to support the antibody-based findings, revealing specific binding in liver, pancreas, and kidney. As a final approach, RNA-sequencing and single-cell RNA (scRNA)-sequencing were implemented. RNA-sequencing confirmed GCGR presence within liver and kidney tissue. The GCGR was specifically found to be expressed in hepatocytes by scRNA-sequencing and potentially also in collecting and distal tubule cells in the kidney. Our results clearly indicate the liver and the kidneys as the primary targets of glucagon action.

Macrophage-derived microRNA-223 Promotes Intestinal Mucosal Barrier Dysfunction via Exosomal Pathways in Inflammatory Bowel Disease

Background & Aim: Exosomes are effective mediators of cell-to-cell interactions and carry many regulatory molecules, including miRNAs, that can play crucial roles in diverse fundamental biological processes. However, to date, no study has reported macrophage exosomal involvement in the development of inflammatory bowel disease (IBD). This study investigated the specific miRNAs in macrophage-derived exosomes in IBD and the potential molecular mechanism. Methods: Dextran sulfate sodium (DSS) was used to generate IBD mice. The supernatants of murine bone marrow-derived macrophages (BMDMs) with or without lipopolysaccharide (LPS) were collected for exome isolation and miRNA sequencing. Lentiviruses were used to modify miRNA expression and further investigate the role of macrophage-derived exosomal miRNAs. In vitro, both mouse and human organoids were applied to a Transwell system in co-culture with BMDMs as a cellular IBD-related challenge.Results: Here, we show that LPS-induced macrophages can release exosomes containing various miRNAs, aggravating IBD. We analyzed miRNA sequencing of macrophage-derived exosomes, and miR-223 was selected for further study. In vivo, exosomes with high miR-223 expression contributed to the exacerbation of intestinal barrier dysfunction, which was further verified in both mouse and human colon organoids. Furthermore, time-dependent analysis of the mRNAs of DSS-induced colitis mouse tissue combined with miR-223 target gene prediction was performed to select the candidate gene, and the barrier-related factor TMIGD1 was identified.Conclusion: Collectively, these data indicated that macrophage-derived exosomal miR-223 played a novel role in intestinal barrier dysfunction by inhibiting TMIGD1 in the progression of DSS-induced colitis.

AngIV-Analog Dihexa Rescues Cognitive Impairment and Recovers Memory in the APP/PS1 Mouse via the PI3K/AKT Signaling Pathway

The renin-angiotensin system (RAS) is a paracrine RAS within the central nervous system (CNS) and is closely related to Alzheimer’s disease (AD). The endogenous hexapeptide angiotensin IV (Ang IV), an important component of the brain RAS, was found to rescue cognitive impairment and recover memory in previous studies. In our study, we used different doses of Dihexa, which can be orally administered and cross the BBB in APP/PS1 mice. We found that the amount of AngIV in mouse tissue increased after the administration of Dihexa compared to that in the WT group. Meanwhile, Dihexa restored spatial learning and cognitive functions in the Morris water maze test. Dihexa increased the neuronal cells and the expression of SYP protein in APP/PS1 mice in Nissl staining. Furthermore, Dihexa decreased the activation of astrocytes and microglia, markedly reduced levels of the pro-inflammatory cytokines IL-1β and TNF-α and increased the levels of the anti-inflammatory cytokine IL-10. Dihexa activated the PI3K/AKT signaling pathway, while PI3K inhibitor wortmannin significantly reversed the anti-inflammatory and anti-apoptotic effects of APP/PS1 mice. These findings highlight the brain AngIV/PI3K/AKT axis as a potential target for the treatment of AD.

Self-distillation contrastive learning enables clustering-free signature extraction and mapping to multimodal single-cell atlas of multimillion scale

Massively generated single-cell multi-omics datasets are revolutionizing biological studies of heterogenous tissues and organisms, which necessitate powerful computational methods to unleash the full potential of these tremendous data. Here, we present Concerto, stands for self-distillation contrastive learning of cell representations, a self-supervised representation learning framework optimized with asymmetric teacher-student configuration to analyze single-cell multi-omics datasets with scalability up to building 10 million-cell reference within 1.5 hour and querying 10k cells within 8 seconds. Concerto leverages dropout layer as minimal data augmentation to learn meaningful cell representations in a contrastive manner. The teacher module uses attention mechanism to aggregate contextualized gene embeddings within cellular context, while the student module uses simpler dense structure with discreate input. The learned task-agnostic representations can be adapted to a broad range of single-cell computation tasks. 1) Via supervised fine-tuning, Concerto enables automatic cell classification as well as novel cell-type discovery; 2) Attention weights provide model interpretability via automatically extracting specific molecular signatures at single-cell resolution without the needs of clustering; 3) Via source-aware training, Concerto supports efficient data integration by projecting all cells across multiple batches into a joint embedding space. 4) Via batch-aware inference or unsupervised fine-tuning, Concerto enables mapping query cells onto reference and accurately transferring annotations. Concerto can flexibly extend to multi-omics datasets simply through cross-modality summation operation to obtain unified cell embeddings. Using examples from human peripheral blood, human thymus, human pancreas, and mouse tissue atlas, Concerto shows superior performance benchmarking against other top-performing methods. We also demonstrate Concerto recapitulates detailed COVID-19 disease variation through query-to-reference mapping. Concerto can operate on all genes and represents a fully data-driven approach with minimum prior distribution assumptions, eliminating the needs of PCA-like or autoencoder-like dimensionality reduction, which significantly reforms the current best practice. Concerto is a simple, straightforward, robust, and scalable framework, offering a brand new perspective to derive cell representations and can effectively satisfy the emerging paradigm of query-to-reference mapping in the era of atlas-level single-cell multimodal analysis.

Quantitative super-resolution microscopy reveals promoting mitochondrial interconnectivity protects against AKI

Background: The root of many kidney diseases in humans can be traced to alterations or damage to subcellular organelles. Mitochondrial fragmentation, ER stress and lysosomal inhibition, among others, ultimately contribute to kidney injury and are the target of therapeutics in development. While recent technological advancements allow for the understanding of disease states at the cellular level, investigating changes in subcellular organelles from kidney tissue remains challenging. Methods: Using structured illumination microscopy, we imaged mitochondria and other organelles from paraffin sections of mouse tissue and human kidney biopsies. The resulting images were 3D rendered to quantify mitochondrial size, content, and morphology. Results were compared to transmission electron microscopy and segmentation. Results: Super-resolution imaging reveals kidney tubular epithelial cell mitochondria in rodent and human kidney tissue form large, interconnected networks under basal conditions, which are fragmented with injury. This approach can be expanded to other organelles and cellular structures including autophagosomes, endoplasmic reticulum (ER), brush border and cell morphology. We find that during unilateral ischemia, mitochondrial fragmentation occurs in most tubule cells and remain fragmented for over 96 hours. Promoting mitochondrial fusion with the fusion promotor M1 preserves mitochondrial morphology and interconnectivity and protects against cisplatin-induced kidney injury. Conclusions: We provide for the first time a non-biased, semi-automated approach for quantification of the 3D morphology of mitochondria in kidney tissue. Maintaining mitochondrial interconnectivity and morphology protects against kidney injury. Super-resolution imaging has the potential to both drive discovery of novel pathobiological mechanisms in kidney tissue and broaden the diagnoses that can be made on human biopsies.

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling

Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). We validated the human and mouse WTA assays using cell lines to demonstrate concordance with orthogonal gene expression profiling methods in profiled region sizes ranging from ~10-500 cells. By benchmarking against bulk RNAseq and single-molecule fluorescence in situ hybridization, we demonstrate robust transcript detection possible down to ~100 transcripts per region. To assess the performance of WTA across tissue and sample types, we applied WTA to biological questions in cancer, molecular pathology, and developmental biology. We show that spatial profiling with WTA can detect expected spatial gene expression differences between tumor and tumor microenvironment, identify spatial disease-specific heterogeneity in gene expression in histological structures of the human kidney, and comprehensively map transcriptional programs in anatomical substructures of nine organs in the developing mouse embryo. Digital Spatial Profiling technology with the WTA assays provides a flexible method for spatial whole transcriptome profiling applicable to diverse tissue types and biological contexts.

Development of a Quantitative FMRP Assay for Mouse Tissue Applications

Fragile X syndrome results from the absence of the FMR1 gene product—Fragile X Mental Retardation Protein (FMRP). Fragile X animal research has lacked a reliable method to quantify FMRP. We report the development of an array of FMRP-specific monoclonal antibodies and their application for quantitative assessment of FMRP (qFMRPm) in mouse tissue. To characterize the assay, we determined the normal variability of FMRP expression in four brain structures of six different mouse strains at seven weeks of age. There was a hierarchy of FMRP expression: neocortex > hippocampus > cerebellum > brainstem. The expression of FMRP was highest and least variable in the neocortex, whereas it was most variable in the hippocampus. Male C57Bl/6J and FVB mice were selected to determine FMRP developmental differences in the brain at 3, 7, 10, and 14 weeks of age. We examined the four structures and found a developmental decline in FMRP expression with age, except for the brainstem where it remained stable. qFMRPm assay of blood had highest values in 3 week old animals and dropped by 2.5-fold with age. Sex differences were not significant. The results establish qFMRPm as a valuable tool due to its ease of methodology, cost effectiveness, and accuracy.

Biosynthesis of the Novel Endogenous 15-Lipoxygenase Metabolites N-13-Hydroxy-octodecadienoyl-ethanolamine and 13-Hydroxy-octodecadienoyl-glycerol by Human Neutrophils and Eosinophils

The endocannabinoids 2-arachidonoyl-glycerol and N-arachidonoyl-ethanolamine are lipids regulating many physiological processes, notably inflammation. Endocannabinoid hydrolysis inhibitors are now being investigated as potential anti-inflammatory agents. In addition to 2-arachidonoyl-glycerol and N-arachidonoyl-ethanolamine, the endocannabinoidome also includes other monoacylglycerols and N-acyl-ethanolamines such as 1-linoleoyl-glycerol (1-LG) and N-linoleoyl-ethanolamine (LEA). By increasing monoacylglycerols and/or N-acyl-ethanolamine levels, endocannabinoid hydrolysis inhibitors will likely increase the levels of their metabolites. Herein, we investigated whether 1-LG and LEA were substrates for the 15-lipoxygenase pathway, given that both possess a 1Z,4Z-pentadiene motif, near their omega end. We thus assessed how human eosinophils and neutrophils biosynthesized the 15-lipoxygenase metabolites of 1-LG and LEA. Linoleic acid (LA), a well-documented substrate of 15-lipoxygenases, was used as positive control. N-13-hydroxy-octodecadienoyl-ethanolamine (13-HODE-EA) and 13-hydroxy-octodecadienoyl-glycerol (13-HODE-G), the 15-lipoxygenase metabolites of LEA and 1-LG, were synthesized using Novozym 435 and soybean lipoxygenase. Eosinophils, which express the 15-lipoxygenase-1, metabolized LA, 1-LG, and LEA into their 13-hydroxy derivatives. This was almost complete after five minutes. Substrate preference of eosinophils was LA > LEA > 1-LG in presence of 13-HODE-G hydrolysis with methyl-arachidonoyl-fluorophosphonate. Human neutrophils also metabolized LA, 1-LG, and LEA into their 13-hydroxy derivatives. This was maximal after 15–30 s. Substrate preference was LA ≫ 1-LG > LEA. Importantly, 13-HODE-G was found in humans and mouse tissue samples. In conclusion, our data show that human eosinophils and neutrophils metabolize 1-LG and LEA into the novel endogenous 15-lipoxygenase metabolites 13-HODE-G and 13-HODE-EA. The full biological importance of 13-HODE-G and 13-HODE-EA remains to be explored.