Human Protein Atlas

Multiplex tissue image of the month - NES in kidney ? The intermediate filament protein nestin (gene: NES) is highlighted in kidney through multiplex immunohistochemistry (mIHC/IF). ? The glomeruli are the main filtration units of the kidney and are composed of tufts of capillaries formed from endothelial cells and podocytes. Utilizing the mIHC/IF kidney panel, nestin (NES) - a cytoskeleton-associated intermediate filament protein - is localized (green) to the cytoplasm of glomerular endothelial cells (magenta) and podocytes (yellow). Other visualized kidney structures include proximal tubular cells (white). ? ? https://lnkd.in/dWS2zRH9

Building a high-resolution map of proteins in sperm Sperm cells are highly specialized for their function in reproduction and have a unique structure among the human cell types. Similarly, the repertoire of proteins that are present in sperm comprise many cell-type specific components. Researchers affiliated with the Human Protein Atlas have started to map proteins in human sperm using immunofluorescence and confocal microscopy to complement and further build on the comprehensive studies of the sperm proteome that so far mainly have been performed using mass spectrometry. This new approach gives a detailed view of the presence and subcellular localization of proteins in sperm, with single-cell resolution. ? Human sperm consists of a head region, which mainly carries the paternal genome and proteins involved in fertilization of the egg, and a tail region, which is essential for motility and navigation. For sperm to be able not only to swim, but also to find their way to the egg, they need to be able to carefully sense their environment and modulate their swimming path accordingly. On the route to the egg, they also need to go through multiple carefully coordinated maturation events in preparation for fertilization. Thus, it is not surprising that sperm cells contain many proteins involved in cell signaling. The signaling pathways in sperm are highly intertwined and not fully elucidated, but they generally converge at careful regulation of intracellular HCO3?, pHi, cAMP and Ca2+, as well as membrane hyperpolarization. ?These need to be controlled both in time, but also in subcellular space, and thus the cell signaling proteins that mediate the control are likely to be highly compartmentalized at the subcellular level. ? One example is the main Ca2+-channel in mammalian sperm, called CatSper. This complex is built from four pore-forming subunits and several accessory subunits. Antibody-based staining of the core subunits, such as CATSPER3 (see figure, left panel), indicates that these proteins are mainly localized to the principal piece of the tail, forming a gradient with higher concentration in the proximal part. In addition, the punctate staining pattern suggests that CatSper is concentrated in distinct patches in the plasma membrane, supporting the idea of carefully organization of CatSper into signaling domains along the flagellum (Chung et al., 2014). Furthermore, antibody-based staining of the accessory subunits indicates that these display variable distribution patterns along the flagellum. For example, CATSPERB (see figure, right panel) is mainly found in the midpiece of the tail. The potential structural and functional implications of this variability remain to be explored, but this is one example that demonstrates the complexity of protein localization in sperm, and the advantage of imaging-based mapping of the sperm proteome. ? https://lnkd.in/d6BxhArp

Festival of Genomics & Biodata The Festival of Genomics & Biodata is UK's largest and the world's fastest growing life sciences event. This year in London HPA affiliated professor Jochen Schwenk was there to present his research on using blood proteomes for molecular health monitoring. The Festival of Genomics & Biodata has over 7,000 attendees from over 55 countries and is now beyond genomics covering a wide range of topics including diagnostics, cancer research, AI, proteomics, multi-omics, and single-cell & spatial analysis. In the Population proteogenomics session professor Schwenk discussed the feasibility of population-scale proteogenomic analysis using self-sampled blood and how it can be used to understand he dynamic nature of the circulating proteome and its relation to health status, disease origins, and individualized responses. https://lnkd.in/d32FjzNH

HPA Tissue resource for Young Minds An article about the HPA has been published in the magazine Frontiers for Young Minds, explaining the Atlas's purpose and work in simple, engaging language. The magazine is aimed at children and teenagers, but anyone curious about how scientists map cells and tissues in the human body will find the article informative. In the article, researchers from the Tissue resource describe how they explore the human body much like Vikings who once explored new lands. Featuring original illustrations and clear, straightforward text, the article explains the process of collecting and preparing tissue samples, followed by detailed analyses to identify the proteins present in various tissues and cells using both IHC and multiplex IHC. Exciting findings from their projects are also highlighted, such as the detection of cancer cells in HGSOC and the identification of proteins in ciliated cells in the fallopian tubes. Sparking curiosity in young minds is both fun and important. Inspired by the opportunity to reach a broader audience, the researchers decided to write for Frontiers for Young Minds as a way to make cutting-edge research accessible and engaging for all. Hopefully, young readers will explore the atlas and enjoy all its beautiful images and figures. https://lnkd.in/dqk7z2-A

Multiplex tissue image of the month - SOX9 in testis The localization of SOX9 in the nucleus of sertoli cells in testis is visualized with multiplex immunohistochemistry (mIHC/IF). Sertoli cells play an important role within the seminiferous ducts of testis, providing mechanical support and nutrients to the developing sperm cells. With the help of the mIHC/IF Sertoli cells panel, it is possible to facilitate high-resolution spatial localization of proteins in different parts of Sertoli cells. Using this panel, SRY-box transcription factor 9 (SOX9) - a transcription factor that is essential for Sertoli cell development - is localized (green) specifically to the nuclei of Sertoli cells. Other visualized structures include Sertoli cell cytoplasm (red) along with the combined staining of spermatogonia and spermatocytes (cyan). Single-cell RNA sequencing data in the Single Cell resource of the Human Protein Atlas supports the mIHC/IF data showing enhanced expression of SOX9 in Sertoli cells. https://lnkd.in/dmSYMMxE

In an Olink-sponsored Labroots webinar on February 4 three key opinion leaders in proteomics will discuss how integrating antibody-based methods with LC- MS ultimately can advance clinical research. In the webinar Advancing proteomics in clinical research with the combined strengths of mass spectrometry and affinity-based methods KTH Professor in Translational Proteomics Jochen Schwenk, together with Professor of Pathology Hanno Steen from Harvard and Staff Scientist Metabolomics and Proteomics Core Ann-Christine K?nig from Helmholtz Center Munich will discuss how the integration of proximity extension assay (PEA), with LC-MS can expand proteome coverage, facilitate biomarker discovery, and streamline the validation process. The webinar will give the opportunity to engage with leading experts in the field and the topics include: How does next-generation affinity-based proteomics dive into low-abundance proteins in plasma and serum to expand proteome coverage? Which are the advantages and challenges of integrating affinity-based methods with LC-MS for comprehensive proteomic analysis? Read more: https://lnkd.in/dVczu5hh

The role of SPP1 + macrophages in hepatocellular carcinoma In a publication in Frontiers in Immunology HPA related researchers investigated the roles of macrophages and T cells in hepatocellular carcinoma (HCC). Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and therefore novel therapeutic strategies relying on immunotherapy would be of great interest for HCC treatment. Despite the progress in the field many advanced HCC patients do not respond to current immunotherapies. To address this issue a deeper understanding of the tumor immune microenvironment (TIME), particularly the functional diversity of liver macrophages and T cells, and their interactions within the TIME is necessary. In this study transcriptomics data and gene co-expression network and regulatory analysis was used to estimate immune cell heterogeneity and its impact on HCC patients' survival. The concurrent analysis of bulk and single-cell RNA-seq data was used to elucidate key biological processes and associated functional cell types in HCC and was able to highlight the role of immunosuppression, with a particular focus on liver macrophages, which emerged as central players in the tumor microenvironment. By integrating bulk and and scRNA-seq the role of SPP1 + macrophages in modulating TIME in liver cancer could be pinpointed and the inhibition effects of SPP1 in HCC-TAM was also demonstrated. Inhibition of SPP1 in tumor-associated macrophages was shown to lead to a shift towards a favorable phenotype and suggests SPP1 as a potential translational target in immunotherapy for HCC. https://lnkd.in/dpiGd6sV

Multiplex tissue image of the month - CIBAR2 in bronchus The sub-ciliary localization of CIBAR2 in ciliated epithelium of the bronchus is visualized by multiplex immunohistochemistry (mIHC/IF). ? Ciliated cells of the bronchus epithelium are among the additional cell types that have been added to the mIHC/IF-based exploration of protein expression in the recent update of the Human Protein Atlas. Using the ciliated cells panel, made up of five markers for different subcellular structures in ciliated cells, CIBAR2 is localized (green) to the transition zone of the ciliated cells of bronchus epithelium. Other visualized cell structures include ciliated cell-specific axoneme (white), basal body (red), cytoplasm (cyan) and nucleus (magenta). ? The spatial expression data is supported by the single-cell RNA sequencing data for CIBAR2 available in the Single Cell resource showing enriched expression in ciliated cells. ? ? https://lnkd.in/gJ64dcxB

TMEM213 - a ′Gene Doe′ of the kidney and salivary gland ? Among the about 20,000 genes giving rise to the human proteome there are still many rather unknown but potentially interesting genes that deserve some extra attention. Here we will focus on TMEM213, a gene with little evidence and specific expression in the kidney and salivary gland. ? There are only eight genes in the Human Protein Atlas classified as group enriched in kidney and salivary gland. Two of them are subunits of the well-known multisubunit enzyme V-ATPase that is responsible for acidifying and maintaining the pH of intracellular compartments and also mediates secretion of protons from renal intercalated cells into the urine to ensure correct urinary acidification. ? TMEM213 on the other hand lacks protein and transcript evidence in UniProt and has no suggested function. That this protein also deserves more attention is however strongly suggested when looking into the data in the Human Protein Atlas. The expression profiles in both bulk and single cell RNA seq show specific expression in kidney and salivary gland and more specifically in distal tubular cells, salivary duct cells, collecting duct cells and serous glandular cells. ? Expression clustering and correlation of tissue and single cell RNA seq data further show TMEM213 to cluster together with other genes known to be related to transmembrane transport in kidney and salivary secretion. These findings have been confirmed on the protein level using immunohistochemistry that show staining of the protein exclusively in salivary gland and tubular cells of the kidney. A more detailed analysis of the expression in the salivary gland using multiplex immunofluorescence shows the protein located in ionocytes and in the large ducts. This might be a starting point to further understand the function of this interesting protein. ? https://lnkd.in/d5ViU_vM