THE HUMAN PROTEIN ATLAS BLOG

Expert review by Tissue Atlas director

2016-06-21   |   0 Comments
Immunocytochemistry Review RNA-seq Tissue Atlas

Cecilia Lindskog, site director of the Tissue Atlas

In January 2015, the Tissue-based map of the human proteome by UhlÚn et al was published. According to Google Scholar, the paper already has more than 400 citations. In a recent editorial by Cecilia Lindskog, the potential utility of the Human Protein Atlas and the Tissue-based map is reviewed.

Cecilia Lindskog is site director of the Tissue Atlas, and you can read more about her and the Tissue Atlas in this blog post from May this year...Read more


Site director with a fascination for patterns

2016-05-16   |   0 Comments
Human Protein Atlas Immunocytochemistry Interview Microarray Proteomics RNA-seq Tissue Atlas

Cecilia Lindskog, site director of the Tissue Atlas

Time has come for the second interview with a researcher within the Human Protein Atlas project. Today we meet Cecilia Lindskog, site director of the Tissue Atlas.

– I have a Master of Science in Biomedicine and a Doctor of Philosophy in pathology from the Faculty of Medicine, Uppsala University. I joined the Human Protein Atlas project in 2006, and also have industry experience in the biotechnology industry, from Oncomark Ltd, Dublin, Ireland.

Cecilia Lindskog┤s main research interests have always been understanding the biology and functions of different organs, and the underlying mechanisms leading to cancer and other diseases...Read more


Aquaporin 9 expression in human tissue

2016-05-10   |   0 Comments
Hepatocellular Carcinoma Human Protein Atlas Liver Tissue Atlas

Protein expression of aquaporin 9 in normal tissues

In a very recent paper in Journal of Histochemistry and Cytochemistry , with researchers from the Human Protein Atlas, it is shown that the expression of aquaporin 9 is limited in normal tissues, and high membranous expression is observed only in hepatocytes.

Aquaporin 9 is known to facilitate hepatocyte glycerol uptake. Murine aquaporin 9 protein expression has been verified in liver, skin, epididymis, epidermis and neuronal cells using knockout mice.

One goal of the current study was to systematically explore the distribution of aquaporin 9 expression in humans...Read more


Analysis of 32 human organs and tissues

2016-04-20   |   0 Comments
Brain Human Protein Atlas Testis Tissue Atlas

A network plot of the tissue enriched (red) and group enriched (orange) genes

In the Human Protein Atlas, there are 32 human organs and tissues analyzed. 2489 of the genes have significantly higher expression in one tissue compared to all other tissue types. Analysis show that testis is the organ with the largest number of tissue-enriched genes, with 1057 genes classified as testis enriched. The specific events and alterations of cell structure during spermatogenesis, and the fact that sperm has the ability to survive outside the male body may explain why testis has the largest number of enriched genes.

The organ with the second highest number of enriched genes is the brain with 381 enriched genes...Read more


Release of Human protein Atlas version 15

2016-04-11   |   0 Comments
HPA15 Release RNA Tissue Atlas Transcriptome

RNA and protein expression overview

Today, a new version, number 15, of The Human Protein Atlas is launched that includes extensive transcriptomics data and a new display view to allow comparisons of human tissue profiles on both the RNA and protein level. In this new version it is possible to do comparisons of primary data from several sources, including external efforts such as the GTEx dataset generated from the Broad Institute in Boston, US.

The GTEx dataset includes more than 1600 postmortem samples from mostly overlapping, but in some cases unique, tissues compared to the Human Protein Atlas consortium...Read more


The urinary bladder proteome defined

2016-04-05   |   0 Comments
Proteome Tissue Atlas Transcriptomics Urinary bladder

Immunohistochemistry-based protein profiling of elevated genes in urinary bladder that are expressed in umbrella cells.

To understand the molecular functions of the urinary bladder, researchers including scientists from The Human Protein Atlas project have recently defined the expression of elevated genes in the bladder.

The main function of the urinary bladder is to store the urine made by the kidneys, allowing urination voluntarily. The urothelium also plays an important role in preventing rupture of urine storage and leakage of toxic urinary substances into the blood...Read more


Potential new tool for measuring beta cell mass

2016-03-29   |   0 Comments
Beta cells Diabetes Pancreas Proteome Tissue Atlas

Immunohistochemical staining of human pancreas shows strong cytoplasmic positivity in islet cells.

In a recent study, scientists including members of The Human Protein Atlas project have identified the beta cell specific protein GPR44 as a potentially novel tool for measuring beta cell mass in vivo, using radiolabeled PET ligands targeting GPR44.

The pancreatic beta cell is responsible for producing insulin and beta cell loss is one of the causes underlying diabetes. Blood biomarkers to measure beta cell function exist, but there is a lack of good tools for measuring the beta cell mass inside the body.

In this study, the ligand targeting GPR44 was compared to a ligand targeting the established beta cell marker VMAT2, and the performance was evaluated...Read more


The uterine endometrium-specific proteome defined

2016-03-22   |   0 Comments
Endometrium Proteome Tissue Atlas

In a recent study by co-workers of The Human Protein Atlas project over 100 genes with elevated expression pattern in the normal endometrium was found. A majority of these genes are well-known and have been extensively characterized. However, the list of endometrium-specific genes also includes uncharacterized genes, providing starting points for further studies of their role in normal homeostasis and diseases affecting the endometrium.

The uterus contains the endometrial mucosa which is the site for embryo implantation...Read more


The human gastrointestinal tract proteome

2016-03-08   |   0 Comments
Gastrointestinal Tract Proteome Tissue Atlas

The gastrointestinal tract (GIT) consists of different organs with many shared functions and characteristics, but also distinct differences.

The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling

In a recent study by scientists from the Human Protein Atlas project and colleagues, a genome-wide transcriptomics analysis combined with immunohistochemistry-based protein profiling was performed to describe the gene and protein expression patterns that define the human gastrointestinal tract (GIT).

The GIT organs (stomach, duodenum, jejunum/ileum and colon) were compared to gene expression levels in 23 other normal human tissues...Read more


Biomarker for prognosis in endometrial carcinoma

2016-03-01   |   0 Comments
ASRGL1 Cancer Endometrial Carcinoma Microarray Tissue Atlas

Reduced expression of ASRGL1 was significantly associated with poor prognosis and reduced disease-specific survival.

Loss of ASRGL1 expression is an independent biomarker for disease-specific survival in endometrioid endometrial carcinoma

The ASRGL1 protein is a novel, powerful, and independent biomarker for prognosis in endometrial carcinoma.

In a recent study by scientists from the Human Protein Atlas project and collaborators at the University of Bergen and University of Turku, the l-asparaginase (ASRGL1) protein was identified as an endometrial carcinoma biomarker candidate by searches in the HPA-database.

ASRGL1 expression was immunohistochemically evaluated on two large independent endometrial carcinoma cohorts using an extensively validated antibody...Read more


The human skin proteome

2016-02-23   |   0 Comments
Proteome Skin Tissue Atlas

The human skin-specific genes defined by transcriptomics and antibody-based profiling

Normal skin is consists mainly of epidermal cells in different phases of de-differentiation (keratinization) organized in several distinct layers with different appearance, functions, and molecular signatures. To characterize the skin-specific genes and the landscape of gene and protein expression in normal human skin in different layers and stages of differentiation, scientists from the Human Protein Atlas project have combined immunohistochemistry-based protein profiling and genome-wide deep sequencing of mRNA to compare skin with other normal tissue types...Read more


The human prostate proteome

2016-02-09   |   0 Comments
Cancer Prostate Proteome Tissue Atlas

The definition of the prostate specific proteome provides a starting point for further studies exploring the molecular repertoire of the prostate.

Novel biomarkers for prostate cancer found while defining the prostate specific transcriptome and proteomeTo better understand the function of the prostate and diseases associated with it, it is important to explore the molecular constituents that make up the prostate gland.

In a recent study by scientists from the Human Protein Atlas project and colleagues both gene and protein expression profiles were investigated in prostate tissue and compared to 26 other human tissues. The aim was to identify potential prostate specific biomarkers for potential clinical use...Read more


A prognosis based classification of uterin cancer

2015-12-01   |   0 Comments
Cancer Microarray Tissue Atlas Undifferentiated uterine sarcoma

The ovaries, fallopian tubes, and uterus

A prognosis based classification of undifferentiated uterine sarcomas: Identification of mitotic index, hormone receptors and YWHAE-FAM22 translocation status as predictors of survival

Undifferentiated uterine sarcomas (UUS) are rare tumors with a heterologous biology and a poor prognosis.

In a recent study by scientists from the Human Protein Atlas project and colleagues, the relevance of clinicopathology, mitotic index, translocation status (YWHAE-FAM22), and a number of biomarker candidates were examined for correlation with the prognosis of these tumors. The protein biomarkers P53, P16, Ki-67, Cyclin-D1, ER, PR, and ANLN were evaluated by immunohistochemistry...Read more


The human cardiac and skeletal muscle proteomes

2015-11-24   |   0 Comments
Heart Proteome Tissue Atlas

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling

To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents to identify similarities and differences in gene expression patterns between these different striated muscle tissues. In an effort driven by scientists from the Human Protein Atlas and colleagues, the genes and proteins with elevated expression in cardiac and skeletal muscle in relation to all other major human tissues and organs were investigate using a global transcriptomics analysis complemented with antibody-based profiling...Read more


Prognostic impact of COX-2 in lung cancer

2015-11-17   |   0 Comments
Cancer COX-2 Lung cancer Microarray Tissue Atlas

COX-2 expression in stroma

Prognostic impact of COX-2 in NSCLC: a comprehensive compartment-specific evaluation of tumor and stromal cell expression

In a study performed by scientists at Uppsala University, in collaboration with Gothenburg University and the Human Protein Atlas project, the expression of cyclooxygenase-2 (COX-2) was evaluated in patients with non-small cell lung cancer (NSCLC)...Read more


Elevated expression of CD93 in brain tumor

2015-11-03   |   0 Comments
Brain cancer Cancer CD93 Glioblastoma Tissue Atlas

CD93 expression in pathological blood vessels in a case of high-grade malignant glioma

Elevated expression of the C-type lectin CD93 in the glioblastoma vasculature regulates cytoskeletal rearrangements that enhance vessel function and reduce host survival

CD93 encodes for a cell-surface glycoprotein and is expressed in myeloid cells and endothelial cells. CD93 has recently been identified as an important gene in primary tumor angiogenesis and the corresponding protein has been shown to have proangiogenic properties. In the present study the role of CD93 in malignant glioma was analyzed. The effect on glioblastoma vessels and tumor growth was studied...Read more


The human brain proteome

2015-10-27   |   0 Comments
Brain Proteome Tissue Atlas

The human brain proteome mapped using transcriptomics and antibody-based profiling with a focus on the cerebral cortex

The mammalian brain is a complex organ composed of many specialized cells, as well as specialized and discretely localized proteins. In a recent study by scientists from the Human Protein Atlas and colleagues, transcriptomics and protein expression data was used to analyze brain-enriched genes from the frontal cortex...Read more


The building blocks of life

2015-10-20   |   0 Comments
HPA13 Science Tissue Atlas

All major human tissues and organs analyzed for protein expression.

Tissue-based map of the human proteomeThe effort to map the human proteome gives new insights on human health and disease.

The Human Protein Atlas, a large-scale multidisciplinary project supported by the Knut and Alice Wallenberg foundation in Sweden, is mapping all human proteins to their location in the body. The project, which was initiated a decade ago, has engaged researchers from many different disciplines and to date annotated over 13 million images showing the localization of our proteins in the human body on a cellular and sub-cellular level. All images and data are publicly available at the web portal Human Protein Atlas...Read more