THE HUMAN PROTEIN ATLAS BLOG
Previously we have highlighted proteins expressed in the human neural retina. Today, we will focus on the lens and shed light on its structure and function, and hopefully spark an interest in you for the proteins of the lens.
The main function of the lens is to focus light on the retina. The passage of light through the cornea, lens and vitreous all the way to the retinal layer of the eye is only possible due to transparency of the tissue. Although the lens is very protein-rich, light absorption and light scattering in the lens is minimal.
The lens comprise of non-diving lens cells which are mainly composed of ordered proteins called crystallins...Read more
Mathias Uhlen from the Human Protein Atlas will on July the 27 present a keynote lecture on the Europe-Korea Conference on Science and Technology (EKC2017) entitled "The Human Protein Atlas - implications for human biology, drug development and precision medicine"...Read more
Let‘s have a look at the protein TPX2, a microtubule nucleation factor that translocates from the nucleus - where it resides during interphase - to the mitotic spindle during mitosis.
The mitotic spindle forms when chromosomes are ready to segregate during cell division and not surprisingly this protein is also found in this specific compartment of the cell! TPX2 is required for the correct formation of the kinetochores that is crucial for the attachment of microtubules, enabling the sister chromatids to be pulled apart...Read more
This week, Scientific American announced ten emerging technologies with innovations that are on the verge of changing society. One of the technologies selected was the Human Cell Atlas, which aims to integrate research exploring the building-blocks of human cells using new emerging technologies. The list of ten emerging technologies was compiled in a collaboration between Scientific American and the World Economic Forum's Expert Network with suggestions from members of the Expert Network, the forum's Global Future Councils and Scientific American's board of advisers...Read more
In this week's image of the week we look at G protein-coupled receptor 17 (GPR17), a member of the G protein-coupled receptor (GPCR) family, whose members serve as important regulators of oligodendrocyte development.
Oligodendrocytes are the cells that mainly provide support and electrically insulate axons in the brain by forming the myelin sheath. During development, these cells progress from oligodendrocyte precursor cells to myelinating mature oligodendrocytes. GPR17, in particular is an oligodendroglial maturation inhibitor since its stimulation arrests mouse oligodendrocytes at a less differentiated stage...Read more
We would like to thank all participants of the CYTO2017 Image analysis challenge co-organized by the Cell Atlas team. And congratulate the winner, Dr. Peng Qiu from Georgia Tech, who at the time of the challenge closing had the top solution for both Challenge 2 and Challenge 3.
Though submissions this year were high-quality, and showcased the multitude of approaches to such a challenge, there is still large room for improvements in the results and some sub-challenges remain entirely unsolved. Therefore, we have decided to keep the challenge open for another year! Improvements in downloads and scoring schemes will be made.
So stay tuned for updates...Read more
Emma Lundberg Director of the Human Cell Atlas, will present a keynote lecture on June 14th, entitled ”The Cell Atlas: A subcellular map of the human proteome” on the 32ndCongress of the International Society for Advancement of Cytometry in Boston, USA.
On this occassion, the CYTO Congress together with the Human Protein Atlas have organized a challenge for analysis of the images from the Cell Atlas, culminating in presentation of results in the final conference session, where participants will present their analytical methods and findings...Read more
In this week’s post, we will highlight proteins specifically expressed in a tissue with extensive plasticity - the female mammary glands. The evolutionary origin of mammary and milk gland-like structures is believed to date all the way back to 300 million years ago, and glandular secretory apocrine-like units in the skin of synapsids, an ancestor to mammals.
The mammary gland develops from the epidermis and is mainly composed of branched columnar and cuboidal epithelial cells that form distinct lobes...Read more
This month we take a closer look at the JAK family. The JAK – or Janus kinases, are intracellular proteins that transduce signals from cytokine receptors via the JAK-STAT pathway. More specifically the JAK family phosphorylates the receptor and thus activates downstream proteins, including transcription factors called STATs (Signal Transducers and Activators of Transcription). These transcription factors then migrate to the nucleus where they regulate transcription of many genes with diverse function, including cell growth, development and differentiation...Read more
Melanoma is a common form of cancer in the skin and among skin cancers it is the most deadly form. Melanoma originates from cells of melanocytic origin and most typically begins as a small intraepidermal tumor (melanoma in situ). As the tumor continues to grow and progress, tumor cells invade the epidermis and eventually spread to regional lymph nodes and subsequently via hematogenic spread to distant organs. Tumor thickness of the primary tumor is the most important determining prognostic factor and thus is early discovery of key importance for survival...Read more
Mathias Uhlen, Director of the Human Protein Atlas program, will present a keynote lecture on May 23 entitled "Tissue-based protein profiles – implications for human biology, drug development and precision medicine " on the 6th Pharmaceutical Science World Congress (PSWC 2017) in Stockholm, Sweden.
The focus of this year┤s world congress will be " Future medicine for one world " including research and development related to systems approaches to drug discovery development and clinical usage...Read more
In a time when vast amounts of bioimaging data are produced in labs around the globe every day, effectively extracting salient information from this growing resource is paramount to understanding complex biological questions. In December 2016 the Cell Atlas was released, mapping the subcellular localization of over 12,000 human proteins and counting. As a part of this effort, gamers within EVE online and scientists in the HPA annotated the subcellular localization of each protein. This has created a massive high-quality atlas of microscopy images together with their subcellular protein localization annotations...Read more
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
Today, you will be introduced to the master gland in the body - the pituitary gland.
The pituitary gland plays a crucial role in human physiology, and together with the hypothalamus this highly conserved and elegant system form a link between the nervous and endocrine system, by controlling the functions of the thyroid, adrenal glands, and the gonads, and also regulating growth, lactation, and water preservation.
The pituitary gland, also called hypophysis, consists of two separate lobes with dual embryonic origin; the anterior (adeno) pituitary gland originates from the oral cavity, and the posterior (neural) pituitary gland develops from the neural plate...Read more
This blog post is in honor of World Malaria Day
When infected mosquitos bite people they transmit parasites that causes malaria. Symptoms of malaria include fever and flu-like illness, and if left untreated the illness will cause anemia (loss of red blood cells) and eventually death.
According to WHO, malaria caused 429 000 deaths in 2015, and 70% of the deaths are children under the age of 5. Luckily, mortality rates are falling, and since 2010 the mortality has dropped with almost 1/3. Early diagnosis and treatment of malaria reduces deaths and prevents transmission. There are antimalaria drugs available, but currently, there is no availabe malaria vaccine...Read more
Today we highlight another part of Swedish or Scandinavian (food) culture - "Taco Fredag" or "Taco Friday". Doesn't sound Swedish to you? But staying in on a Friday night and having tacos with your family and/or friends is a thing here, and a big thing as it happens, with supermarkets having entire sections dedicated to this tradition.
So what other image to look at in this week's edition of the Human Protein Atlas blog than the one representing TACO1. TACO1 acts as a translational activator for the mitochondrial encoded cytochrome c oxidase 1, which is a component of complex IV of the mitochondrial respiratory complex...Read more
Today we meet yet another researcher within the Human Protein Atlas project, Johan Rockberg, Associate Professor in antibody technology and directed evolution at KTH - Royal Institute of Technology in Stockholm, Sweden. He is the group leader for the epitope mapping and therapeutic antibodies group within the Human Protein Atlas.
– I have a M. Sc in chemical engineering from KTH and University of Sydney and joined the Human Protein Atlas Project in 2003, right in the beginning. Since I took courses in computational and information science in parallel with chemical engineering it was natural to pursue a career in bioinformatics...Read more
A team from the Human Protein Atlas is attending the AACR Annual Meeting 2017 in Washington DC right now. This year, the meeting covers topics on research propelling cancer prevention and cures, and the Human Protein Atlas is represented by a booth where our team gives a personalized go-through of the Atlas to everyone who is interested in our open access resource. In addition, a demo version of a new Pathology Atlas can also be previewed in our booth. It will contain information on the prognostic genes and proteins for clinical outcome of the major cancer types in humans...Read more
It is Friday, and time for another image of the week, today from our Cancer Atlas group!
Renal cell cancer is a relatively common form of human cancer. Tumors develop in the kidney and have a tendency to grow into renal veins and metastasize to distant organs without the spread to regional lymph nodes as is common for many other tumor types. This particular case shows a papillary form of renal cell cancer that grows with papillary excrescences into cyst formations and with areas of necrosis.
This tumor has been stained with an antibody (HPA005785) that recognizes the CD44 protein...Read more
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
Welcome back to the Tissue Image of the Month.
This week we will focus on a complex and delicate tissue in our body, namely the retina!
More than a century ago, Cajal published his groundbreaking work on the retina. At that time, Cajal was eager to confirm previous observations he had made in other neural tissues, and he considered the retina very suitable to study due to its simple organization and structure.
The human retina is a multilayered neural tissue that originates from the developing brain, and populates the innermost layer of the eye, called the inner photosensitive layer...Read more
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
Researchers from the Human Protein Atlas are planning a clinical trial of a new treatment for nonalcoholic fatty liver disease and type 2 diabetes which harnesses liver cells own ability to burn accumulated fats.
In a study involving 86 patients with varying degrees of fatty liver disease, researchers found that the liver has the ability to burn up accumulated fats. The researchers propose a mixture of substances that will set this process in motion.
Assistant Professor Adil Mardinoglu says the team┤s metabolic modeling approach, which relied on data from the Human Protein Atlas project, can be used for a number of chronic liver diseases...Read more
This week we highlight a new structure in the Cell Atlas available in version 16 thanks to the annotations done by citizen scientists in Project Discovery, a mini game within EVE Online. Rods & Rings.
As the name describes, these unique structures that form large rod and ring type aggregates in the cytoplasm that look a bit like sprinkles. Little is known about this structure and the proteins that are involved in it. In fact, it wasn't until 2011 when the term "Rods & Rings" was coined (Seeling HP et al. 2011,Carcamo WC et al. 2011)...Read more
A new research program has been started to produce all the human secreted proteins in mammalian cell factories. The program aims to facilitate studies of this important class of proteins involved in many human diseases.
The human secreted proteins, sometimes called the "secretome", consist of approximately 3000 proteins, which are produced inside our cells and then often transported out to the blood. This class of proteins is important in many central processes in humans, including bacterial and viral defense, inflammation, cell signaling and transport of nutrients...Read more
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
This month, the online magazine Labiotech.eu writes about scientists who translates science from academia to the market. While there are a many academic entrepreneurial superstars in the US, Labiotech.eu points out that there are also some academic researchers in Europe that have been successful in taking their findings into the biotech industry and lists ten individuals in Europe who have been successful at co-founding biotech companies.
Out of these ten persons, no less than three have connections to Sweden. Emanuelle Charpentier, co-discoverer of CRISPR, did some of her findings at Umeň University...Read more
In 2017, February 28th will be the day that in Sweden is known as "Fettisdagen", (lit. "Fat Tuesday"), in other countries known as "Mardi Gras", "Faschingsdienstag" or "Shrove Tuesday". This day was originally celebrated in the Christian tradition as the last day of a three day feast to prepare for the forty day long fasting period before Easter. Today it has been popularized and in many places around the world this day is now known for its carnivals.
In Sweden together with some other northern European countries we like to eat "semlor" on Fat Tuesday...Read more
The term precision medicine describes the idea of providing effective treatment based on a patient´s molecular make up.
Eculizumab is used to treat patients with paroxysmal nocturnal hemoglobinuria (PNH) and atypical haemolytic uremic syndrome (aHUS). However, eculizumab is a very expensive drug, and the treatment is not efficient for all patients...Read more
Tissue Atlas group is pleased to announce the launch of the Tissue Image of the Month. Previously, you have had the joy of experiencing interesting images of cellular organelles and proteins described by the Cell Atlas. Now we also hope that you will follow the blog posts and pictures of stained tissues with the same excitement and curiosity, as we dive into the world of histology, immunohistochemistry, cells and tissues.
First up - hairs and hair follicles.
Hair fibers consist of cells called trichocytes. The fibers vary in size, disposition and color due to factors such as age, sex, ethnicity and region of the body...Read more
In the latest version of the Human Protein Atlas, released in December 2016, the tissue atlas data is complemented with RNA-data from The Functional Annotation of Mammalian Genomes 5 (FANTOM5) project in RIKEN, Japan. The FANTOM data greatly overlaps with the Human Protein Atlas data, strengthening the results from both the projects.
The human genome consists of DNA which is transcribed into functional protein-coding transcripts (mRNA) and in turn is translated into proteins, the functional building-blocks of the cell. The entirety of mRNA molecules in a cell or tissue is called the "transcriptome"...Read more
Today we meet Hanna Tegel, site director at the AlbaNova site of the Human Protein Atlas, and group leader of the Antigen and Antibody Factory group. She has been with the Human Protein Atlas from the very beginning, and her career has evolved alongside the project.
– I took my M.Sc. in biotechnology at KTH – the Royal Institute of Technology here in Stockholm, and in the end of my education I complemented it with some physiology at the Karolinska Institute. As a part of this course I did a project at KTH, and when it was time for me to do my masters thesis I turned to the same professor. Now he was involved in the start-up of the Human Protein Atlas project...Read more
In a recent publication in Journal of Proteome Research, researchers from the Cell Profiling group of the Human Protein Atlas team present a new approach for validation of antibodies for bioimaging applications.
Antibodies are indispensible research tools, yet the scientific community has not adopted standardized procedures to validate their specificity. Here the researchers present a strategy to systematically validate antibodies for immunofluorescence applications using gene tagging.
Marie Skogs is the first author of the study.
– After a M. Sc...Read more
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
During the Precision Medicine World Conference in Silicon Valley on January 23-25, Mathias Uhlen, leader of the Human Protein Atlas will give a talk about the recently initiated SCAPIS – SciLifeLab Wellness Profiling project.
The Precision Medicine World Conference is a conference series that attracts recognized leaders, top global researchers and medical professionals, and innovators across healthcare and biotechnology sectors to showcase practical content that helps close the knowledge gap between different sectors, thereby catalyzing cross-functional fertilization and collaboration...Read more
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