THE HUMAN PROTEIN ATLAS BLOG

A subcellular map of the human proteome

2017-05-12
Cell Atlas Immunocytochemistry Immunofluorescence Organelle Science

30 organelles and substructures are annotated in the Cell Atlas.

The Cell Atlas database was just recently released with data on more than 12.000 proteins and mapping to 30 organelles. Today, the scientific findings are published in Science in "A subcellular map of the humanproteome".

The cell is a complex entity that carries out multiple functions. In order to do this, the different parts of the cells are organized in structures, called organelles. By investigating the organelles and its proteome, and to understand how the proteins vary over time and space we can truly begin to understand human biology on a detailed level...Read more


Tissue Atlas: microscopy and annotation

2017-03-28
Annotation Immunocytochemistry Microscopy Tissue Atlas

Borbala Katona at the microscope

Today, we are back in the Tissue Atlas facilities at the Rudbeck lab in Uppsala. Borbala Katona and Maria Aronsson are research engineers in the group working with microscopy and annotation of stained tissues, which we described last week.

Borbala Katona has a bachelors degree in biomedicine and a masters degree in infectious medicine and has been working within the Human Protein Atlas since 2014.

Maria Aronsson has a masters degree in medical biology from Link÷ping University and joined the Human Protein Atlas in 2012...Read more


Tissue Atlas: production and staining

2017-03-21
Antibody Immunocytochemistry Tissue Atlas

Today, we start a "mini-series" about our Tissue Atlas here at the blog. Join us on a tour through the lab, meet some of the people working there, and see some really nice images produced by the scientists.

All the work on our Tissue Atlas is done at our Uppsala site, with Cecilia Lindskog as site director. You can learn all about her in one of our previous blog posts.

First we meet research engineer IngMarie Olsson who is group leader for the Tissue Microarray Production, Immunohistochemistry, and Scanning-group...Read more


Image of the week from the Cancer Atlas

2017-03-03
Cancer Atlas Image of the week Immunocytochemistry Lung cancer

Today, it is time for the first image of the week from the Cancer Atlas!

Lung cancer is one of the deadliest and most common forms of human cancer. Different forms of lung cancer exist and non-small cell lung cancer is the most common form. The cancer image this week is selected from such a lung cancer that has been immunohistochemically stained for the proliferation marker Ki-67 (MKI67). Ki-67 is the most commonly used immunohistochemical marker in rutin cancer diagnostics. The Ki-67 antigen is expressed in all cell nuclei that are active in the cell cycle and thus positive staining in a tumor cell population reflects the level of proliferation in that particular cancer...Read more


Cancer biomarkers identified

2017-01-23
Biomarkers Breast Cancer Cancer Immunocytochemistry Renal Cell Carcinoma

Gabriela Gremel, involved in both studies on cancer biomarkers

In two recent publications the group of Fredrik PontÚn in Uppsala has identified two very strong, independent biomarkers for the prognostic stratification of breast cancer and renal cell carcinoma.

Renal cell carcinoma is the most common type of cancer affecting the kidney and there is an unmet clinical need for better prognostic and diagnostic tools for it. Diagnosis and subtyping of renal cell carcinoma are achieved through the morphological analysis of tumor sections. The application of immunohistochemistry can reveal important additional clues during the diagnostic work-up...Read more


The human adrenal gland proteome defined

2017-01-11
Adrenal gland Immunocytochemistry Proteome RNA-seq

The adrenal glands are small endocrine glands located right on top of the kidneys. Each gland has two parts, the adrenal cortex and the adrenal medulla.

In a recent publication in Endocrinology, researchers from the Human Protein Atlas have performed a comprehensive analysis of the gene expression landscape of the adrenal glands to define genes with different degrees of "specific" expression compared to 31 other normal human organs and tissue types. The analysis showed that only 253 genes (approximately 1% of all putative protein coding genes) showed some level of adrenal gland specific expression pattern.

The adrenal gland is a composite endocrine organ with vital functions that include the synthesis and release of glucocorticoids and catecholamines...Read more


The cancer proteome

2016-08-09
Cancer Immunocytochemistry Proteome

Tumor protein p53 in colorectal cancer

Cancer can be defined as a common heterogeneous and potentially deadly disease that affects approximately 1/3 of the human population. The common denominator for cancer is the development of an uncontrolled growth of cells that eventually leads to multiple organ failure and death.

The cancer proteome is based on genes that are implicated in cancer. Expression of these genes in normal cells contributes to normal growth, survival and function, whereas dysregulated expression, including overexpression, loss of expression or expression of a defect protein in cancer cells contributes to ungoverned tumor growth...Read more


Expert review by Tissue Atlas director

2016-06-21
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
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


Systematic antibody validation using siRNA

2016-02-02
Cell Atlas Gene editing Immunocytochemistry Immunofluorescence siRNA Subcell Atlas

Fig 1a. The protein HNRNPUL1 is localized to the nucleus by staining with antibody HPA046290 (green)

Systematic antibody validation with siRNA for the Human Protein Atlas

Antibodies are among the most frequently used tools for basic research and clinical assays. For antibodies used in therapy or diagnostics, there are well-defined and strict guidelines that must be complied with before approval for clinical assays. For research antibodies, such guidelines have not yet been developed, despite the importance of demonstrating that they are specific, selective, and yield reproducible results in the immunoassay for which they are to be used...Read more


Validation of antibodies using GFP-tagged target

2015-12-15
Cell Atlas Co-localization HPA14 Immunocytochemistry Immunofluorescence Subcell Atlas Validation

Antibody HPA37362 targeting BOD1L1 overlaps with GFP-tagged target protein and the localization is identical to that of endogenous protein in non-transfected control cells

Version 14 of The Human Protein Atlas includes a new type of validation of antibodies that are used for determining the subcellular localization of a protein.

A set of antibodies have been analyzed in transgenic cell lines expressing GFP-tagged target protein at near-endogenous levels to confirm that the antibodies are capable of binding the target protein. The approved antibodies are then used to determine the subcellular localization of endogenous protein in a selection of cell lines. A high validation score is assigned to those genes where the same location(s) are observed for both tagged protein and protein detected using labelled antibody in non-transfected cells...Read more


Increasing reliability by co-localization

2015-11-10
Cell Atlas Co-localization HPA14 Immunocytochemistry Immunofluorescence Subcell Atlas Validation

Subcellular localization obtained using IF (left) and GFP (FP, right) for the endoplasmic protein FKBP7 (top) and the FHL2 protein localized to focal adhesion sites (bottom).

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells

The Human Protein Atlas applies antibodies for a variety of applications to map protein expression in different tissues and also at the subcellular level. Within the subcellular protein atlas, immunofluorescence (IF) is used to uncover the localization of proteins to different organelles. To ensure an accurate localization of each and very protein, the antibodies have to be specific to their target protein...Read more