THE HUMAN PROTEIN ATLAS BLOG
The American Society for Cell Biology (ASCB) and the European Molecular Biology Organization (EMBO) jointly organize the first international conference on cell biology of brain. The ASCB/EMBO meeting takes place in Philadelphia on the 2-4 of December 2017.
The conference brings together a program covering presentations from molecular structure and function analysis to signalling pathways, immunity and cellular interplay in organoids.
At the meeting, Dr. Emma Lundberg presents "What is an atlas and why is it important to build?" in a subgroup aiming to discuss the creation of a multiscale, multidimensional Human Cell Atlas...Read more
Staining of NFIL3 (green) in nuclear bodies with DNA (blue) and microtubules (red) in A-431 cells. Many human genes follow a so called circadian clock and research has shown that some of those genes themselves follow the seasons (Dopico et al. 2015). When winter is coming, you sense it and your genes know it too. Expression of one of those genes, NFIL3, peaks during December until February and has its lowest expression during the summer months.
NFIL3 is a transcriptional regulator involved in regulation of immune processes. Like many other transcription regulators it localizes to nuclear bodies as seen on the Cell Atlas images and binds to specific DNA motifs...Read more
Next in our series of articles on cancer is Pancreatic cancer, a relatively rare cancer associated with very poor prognosis. The vast majority of tumors originate from ductal cells and a small fraction are endocrine tumors. Over 80% of pancreatic cancers develop at ages above 60 years and most tumors are detected at late stages of the disease when the cancer has spread beyond the pancreas.
There is a great need for biomarkers to facilitate early detection and help establishment of diagnosis. Smoking, obesity, physical inactivity and long-lasting inflammation in the pancreas are some of the factors that lead to an increased risk of pancreatic cancer...Read more
At the EMBO|EMBL symposia "From Single to Multi-omics: Applications and Challenges in Data Integration" in Heidelberg, Germany, on November 13, Dr Linn Fagerberg presents the talk entitled "Integrative omics profiling within the Swedish SCAPIS SciLifeLab (S3) Wellness Profiling program". The talk focuses on the integration of data retrieved from the analysis of biological samples collected within the SCAPIS project using different technological platforms. On the same day, Dr Fredrik Edfors participates in the poster session with a poster entitled "Gene specific correlation between protein and RNA"...Read more
A key feature and a critical first step in understanding cell division and proliferation lies in characterizing the temporal regulation of protein abundance. A collaborative publication "Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS" was recently published in eLife.
The Cell atlas team from Sweden joined forces with Dr Tony Ly and Professor Angus Lamond from the University of Dundee, to perform a proteome-wide analysis of changes in protein abundance and phosphorylation across the cell cycle...Read more
Dr Cecilia Lindskog, presents a plenary lecture on October 31 entitled "The Human Protein Atlas - implications for human biology and precision medicine" on the Clinical Proteomics, Postgenome Medicine conference in Moscow, Russia. Dr Lindskog is highlighted as one of the key speakers of the conference.
The 300+ international participants at the conference include medical advisors, scientists and business representatives to bridge translation of research findings to clinical use. The conference opens the fields of "omics" science (genomics, transcriptomics, proteomics, metabolomics) to clinical practioners...Read more
The Human Protein Atlas at the Science for Life Laboratory (SciLifeLab) are teaming up with the Chan Zuckerberg Initiative to strengthen research in cell biology and proteomics.
The Chan Zuckerberg Initiative, which was founded by Facebook founder Mark Zuckerberg and his wife, Dr. Priscilla Chan, provides financial and engineering support for the Human Cell Atlas, an ambitious international collaboration that aims to create a reference atlas of all cells in the healthy human body as a resource for studies of health and disease...Read more
As part of the release Pathology Atlas release, the Human Protein Atlas will each week present a brief and informative summary highlighting genes with prognostic association in different cancer forms. This week, we will focus on Lung cancer one of the deadliest cancers in the world today.
Lung cancer patients have a poor outcome with a 5-year survival rate of 13.6% in men and 19.4% in women. Late diagnosis and lack of effective treatments are considered to contribute to poor prognosis. Smoking is the leading risk factor and is responsible for 70-90% of the lung cancer cases. Lung cancer can be divided into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC)...Read more
The last decades of technical development and availability of protein and peptide microarrays have enabled large-scale profiling of antibodies and precise determination of their specificities through epitope mapping. This has enabled characterization of the human immune response and the produced antibodies. Beside exploring the auto-antibody repertoire, this approach also identifies key autoantigens targeted by the antibodies in e.g. neurodegenerative disorders...Read more
The importance of mapping the human cell has become recognized as one of the key challenges in modern biology. Image-based assays offer a data-rich medium of studying cells and their proteins in situ. As such, several large-scale initiatives for studying cellular biology using image-based assays have been founded in recent years...Read more
We are proud to announce that in 2020, Stockholm will be hosting the world's largest international conference within the area of proteomics: the 19th Annual World Congress of HUPO. The Human Proteome Organization (HUPO) is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training.
This is the first time the HUPO conference is held in Sweden. In addition to the very interesting science that will be presented, you will also experience one of the most beautiful capitals in the world, Stockholm...Read more
In this week's Pathology Atlas blog post, we highlight genes with prognostic association to ovarian cancer , as September is National Ovarian Cancer Awareness Month in the US. Ovarian cancer is the fifth most frequent cause of cancer death in women, and 50% of all ovarian cancers are diagnosed in women older than 65 years of age.
Epithelial ovarian carcinoma is one of the most common gynecologic malignancy. There are five subtypes of epithelial ovarian carcinoma, of which high-grade serous carcinoma is the most common...Read more
As part of the release of the Pathology Atlas, the Human Protein Atlas Blog presents brief and informative summaries of most cancers, and highlight genes with prognostic association in the different cancer forms. The Pathology Atlas is an open access database which includes quantitative transcriptomics data and spatial proteomics data of the major human cancer types that have been analyzed using a systems level approach.
We focus on prostate cancer in this week's blog post to highlight Prostate Cancer Awareness Month in North America and the European Prostate Cancer Awareness Day on the 27th of September...Read more
The Swedish Research Award 2017 has been awarded to Professor Mathias Uhlen by the foundation Research!Sweden. On the September 25th Mathias Uhlen will receive the award for research accomplishments regarding mapping of human proteins within the Human Protein Atlas. The mission of the Research!Sweden foundation is to raise awareness regarding the importance of medical research - for health and prosperity by honoring every year one researcher or politician with the award.
Anna Nilsson Vindefjärd general secretary of Research!Sweden motivates the nomination "Mathias Uhlén's research is extremely valuable both for today and future precision medicine...Read more
Next week on the 17th to 21th of September, the human proteome organization (HUPO), is hosting the 16th HUPO World Congress in Dublin, Ireland. Several Human Protein Atlas-associated researchers will attend the meeting and represent the project in various sessions, including plenary and invited lectures, oral presentations and poster sessions.
HUPO is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training...Read more
The Knut and Alice Wallenberg Foundation (KAW) cellebrates 100-years anniversary of funding research within natural sciences, technology and medicine. Since 1917, when KAW was established, grants have been awarded to enpower both scientific research and education beneficial for the society. Today the foundation is one of the largest private funders of scientific research in Europe.
The KAW funded Molecular Life Science - anniversary symposium is organised by the Royal Academy of Sciences together with KTH - The Royal Institute of Technology, Karolinska Institute and Stockholm University...Read more
The Pathology Atlas, recently published in Science presents key proteins associated with different cancer types. This week's news article will focus on breast cancer and proteins related to cancer prognosis.
Breast cancer is the most common invasive cancer form in women worldwide. The cancer can roughly be classified as ductal or lobular breast cancer depending on the origin. The majority of breast cancers develop sporadically, but for 5-10% of patients there is an inherited factor associated with increased breast cancer risk, namely the BRCA1 and BRCA2 genes. Women with abnormal BRCA1 or BRCA2 have higher risk of developing breast cancer...Read more
This weekend Amsterdam is hosting the 29th European Congress of Pathology (ECP 2017). Fredrik Ponten, Co-Founder and Clinical Director of the Human Protein Atlas program, will present a lecture on September 3 entitled "Tissue-based map of the human proteome as tool for pathology". The focus of this year´s European congress will be "Pathology for Patient Care" highlighting the added value of the pathology science and discipline in providing care and improving health outcomes for patients and population. The congress is expected to provide updates on all aspects of diagnostic and molecular pathology...Read more
Last week the Human Protein Atlas portal was updated with a new Pathology Atlas - an interactive atlas where the expression of specific genes and their influence on patient survival in the 17 major cancer types can be explored. The Pathology Atlas includes quantitative genome-wide transcriptomics data (RNA-seq) of the 17 cancers coupled with clinical outcome and spatial proteomics data (immunohistochemistry) of more than 15,000 proteins.
During the next weeks, we will highlight different cancer types included in the analysis and also show examples of genes with unfavourable and favourable prognostic significance. This week's news article features colorectal cancer...Read more
A new Pathology Atlas is launched today with an analysis of all human genes in all major cancers showing the consequence of their corresponding protein levels for overall patient survival. The difference in expression patterns of individual cancers observed in the study strongly reinforces the need for personalized cancer treatment based on precision medicine. In addition, the systems level approach used to construct the Pathology Atlas demonstrates the power of "big data" to change how medical research is performed.
The dream of personalized treatment for cancer patients takes a major step forward today with the launch by Swedish researchers of the Human Pathology Atlas...Read more
ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers. The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. Ultimately, it will help them gain new insights into how living organisms work.
On July 25, 2017, ELIXIR announced the selected list of ELIXIR Core Data Resources...Read more
Previously we have highlighted proteins expressed in the human neural retina. This week's article emphasizes the cellular structure and molecular dynamics 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 comprises 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
TPX2 was identified in 1997 as a 100 kDa nuclear protein. In cells TPX2, a is 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. Due to its function TPX2 expression is cell-cycle dependent...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
The G protein-coupled receptor 17 (GPR17) was first identified in samples extracted from the central nervous system. This protein belongs to the G protein-coupled receptor (GPCR) protein 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...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
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.
The cancer image of the month shows skin with growth of a cutaneous melanoma...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
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.
This 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
Mitochondria harbors an own genome that renders key proteins involved in production of energy through oxidation of various substrates. Majority of the disorders associated with mitochondrial function are caused by impaired expression of the proteins encoded in the mitochondrial genome. One of these proteins is the translational activator of cytochrome c oxidase 1 (TACO1).
Experimental results reveal that TACO1 is expressed in all tissues within the human body. The protein is detected mainly in the cytoplasm and more precise inside mitochondria. Explore expression and subcellular localization of TACO1 in the Cell Atlas...Read more
Within the Human Protein Atlas project, antibodies are used to study the localization of protein in human tissues and cells. To generate the antibodies recombinant expression clones are produced from human RNA pools by cDNA synthesis, cloning and plasmid purification. These clones produce what is called Protein Epitope Signature Tags (PrESTs), a selected part of the target protein that should be recognized by antibodies.
Johan Rockberg, Associate Professor in antibody technology and directed evolution at KTH - Royal Institute of Technology in Stockholm, Sweden is the group leader for the epitope mapping and therapeutic antibodies group within the Human Protein Atlas...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. The Human Protein Atlas is represented by a booth where researchers give a personalized tutorial of the portal to interested visitors. In addition, a demo version of a new Pathology Atlas containing information on prognostic genes and proteins associated with clinical outcome. The Pathology Atlas focuses on 17 major cancer types in humans...Read more
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. The tumor has been stained with an antibody (HPA005785) that recognizes the CD44 protein.
CD44 is a cell-surface glycoprotein and a receptor for hyaluronic acid that is involved in cell-cell interactions, cell adhesion and migration...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 Linköping University and joined the Human Protein Atlas in 2012...Read more
More than a century ago, Piccolino M. 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. The retina is composed of polarized photosensitive neurons called rods and cones...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 Umeå 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 Pontén 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
The year of 2016 is coming to an end. We have published 76 blog posts (77 with this one), on everything from Project Discovery to proteomics in narcolepsy, obesity and cancer, portraits of our researchers and of course several Images of the Week.
During the year we have released two new versions of the database, where RNA-seq data from the Genotype-Tissue Expression (GTEx) consortium from 28 different tissues with a corresponding tissue in the Human Protein Atlas have been included, and a new Cell Atlas with spatial location of more than 12,000 genes to 30 different organelles and cellular structures was launched...Read more
Over the last couple of months, you have hade the pleasure to see Image of the week here on the blog, where an image we find particularly interesting has been shown and discussed. Now that our Cell Atlas is out, you can browse images of your favorite protein directly in our database! In addition to all the images we have added, there are also new "Human Cell" chapters, which provide a knowledge-based analysis of the human cellular proteomes and an entry into the Human Protein Atlas from different perspectives...Read more
Yesterday our new Cell Atlas was released, at the American Society of Cell Biology Meeting. The Cell Atlas is an open-access interactive database with unparalleled high-resolution images. It visualizes for the first time the location of over 12,000 proteins in cells – opening the way to spatial proteomics, an exciting new discipline predicted to lead to a fundamental increase in our understanding of human health and disease.
Prof Mathias Uhlen, Director of the Human Protein Atlas explains:
– After the genome projects that has characterized the number of human protein-coding genes, the next step is to elucidate the function of these proteins...Read more
Over the last couple of weeks, readers of this blog have learnt about how we culture cells, and how we prepare them for microscopy. This week, the time has come to look into the actual imaging.
Martin Hjelmare is lab manager in the Cell Profiling group, and has worked within the Human Protein Atlas since 2007, the first couple of years in the protein factory, and since 2008 in the Cell Profiling group.
– In the protein factory I learnt a lot about basic lab routines; up scaling of protein expression, coupling columns, running gels, etc. This was very useful when I started working in the group of Emma Lundberg...Read more
To prepare all the images for the Cell Atlas, released on December 4, the cells used are primed for staining and microscopy. Sample preparation is an important step when performing immunofluorescence studies. If wrongly applied it can not only cause unsuccessful detection but also generate misleading information.
The sample preparation performed by the Cell Atlas team includes cell fixation, permeabilization, and immunostaining with primary and secondary antibodies.
– The fixation is the crucial step, and different fixation protocols work better for different sets of proteins, Christian Gnann, a research engineer in the Cell Profiling group explains...Read more
The Human Cell Atlas, to be released on December 4, displays high resolution, multicolour images of immunofluorescently stained cells. This provides spatial information on protein expression patterns on a fine cellular and subcellular level. From the start three cell lines, U-2 OS, A-431 and U-251 MG, originating from different human tissues were chosen to be included in the immunofluorescent analysis...Read more
In less than one month from now, we will release a new version of our database, HPA16! The biggest news is the introduction of a brand new Cell Atlas. It will be an image-based atlas over the subcellular distribution of the human proteome.
– Cells are the machinery of life. Much of the bustling activity in the human cell results from proteins performing specific tasks in designated compartments, the organelles. The Cell Atlas that we are creating will be image-based and describe the subcellular distribution of the human proteome, says Emma Lundberg, Director of the Cell Atlas...Read more
In a recent study in Journal of Proteome Research by Human Protein Atlas-researchers a new reactive epitope of a prostate specific protein, particularly reactive in the late stages of prostate cancer is identified.
According to WHO, prostate cancer is the second most incident cancer in men and the fifth leading cause of death in men worldwide, and there is a demand for novel targets and approaches to diagnose and treat this cancer type. Five-year survival is reached by almost 100% of patients if the disease is still at a local and regional stage; however, the survival rate drops down to 30% in the case of aggressive form with distant metastasis and relapse after treatment...Read more
This week we look at a very spooky protein, BAT3 which localizes to the nucleoplasm (looks like jack o'lanterns if you squint hard enough) and cytoplasm of the cell as seen in Figure 1 in A-431 cells.
In addition to having a spooky name, this protein, also known as BAG6, was first identified as being involved in programmed cell death (apoptosis). Subsequent studies have revealed that BAT3 plays a role in many important cellular processes including gene regulation, protein synthesis, protein quality control, and protein degradation (Binici J & Koch J. 2014)...Read more
Several previous reports have concluded that RNA levels cannot be used to predict protein levels. However, in a new study from KTH Royal Institute of Technology, published in the journal Molecular Systems Biology scientists from the Human Protein Atlas show that protein levels can be predicted from RNA levels if a gene-specific RNA-to-protein factor is used.
The human genome consists of DNA, a molecule that contains the instructions needed to build and maintain cells. For the instructions to be carried out, DNA must be read and transcribed into RNA transcripts that can be used to produce protein. The transcriptome is a collection of all the transcripts present in a cell...Read more
It's time for another HPA image of the week! This week we would like to tease an annotation that is not yet publicly available, but is coming soon in the December 4 release of the Cell Atlas.
During the cell cycle, each chromosome containing your DNA replicates. During mitosis, each chromosome lines up with its copy in the middle of the cell. At this point, the copies of each chromosome are pulled apart from each other via a structure called the mitotic spindle. In order for this chromosomal separation to happen correctly, the two copies of each chromosome must be attached to the microtubules via the kinetochore ( DeLuca J.G. et al 2002)...Read more
In a recent study, published in Blood, researchers have used affinity reagents from the Human Protein Atlas project to analyze plasma samples to identify candidate protein markers associated with risk of venous thromboembolism.
Venous thromboembolism is the third most common cardiovascular disease and a leading cause of death and disability worldwide. Complex interactions between genetic, environmental and acquired risk factors underlie disease development. The first step in the process of developing clinically applicable predictive tools is the identification of novel markers that associate with the disease...Read more
In a recent publication in Cell Systems researchers have identified endothelial biomarkers that provide potential vascular drug targets and candidates for functional studies to increase understanding of the endothelium in health and disease.
Endothelial cells line the inside of all vessels and have a critical role in the regulation of hemostasis, inflammation, defense against blood borne pathogens, vascular tone, angiogenesis, and the transport of molecules and nutrients to and from the blood stream.
Proteins critical for these specialized functions tend to be predominantly expressed in endothelial cells across vascular beds...Read more
This week the 2016 Nobel Prize in Physiology or Medicine was announced and has been awarded to Yoshinori Ohsumi for his work in with understanding autophagy. Congratulations to Dr. Ohsumi on his well deserved award! Please read the link above for a great and brief explanation of Dr. Ohsumi's contributions and other important discoveries related to autophagy.
This week we highlight DNA damage regulated autophagy modulator 2 (DRAM2), a well known inhibitor of autophagy. Figure 1 shows an example of DRAM2 in U2 OS human osteosarcoma cells...Read more
The Human Protein Atlas has since the first array validated antibody in November 2004 now passed 50 000 protein microarray validated antibodies.
The Human Protein Atlas contains information for a large majority of all human protein-coding genes regarding the expression and localization of the corresponding proteins based on both RNA and protein data. For the protein data, antibodies are used to show localization, and now 50 000 antibodies have been produced and verified within the project.
– This is a true heroic effort, says professor Peter Nilsson, site director at the SciLifeLab-site in Stockholm...Read more
In a recent study published in Proteomics Clinical Applications researchers from the Human Protein Atlas have profiled 280 brain-enriched proteins in cerebrospinal fluid from patients with Alzheimer´s disease, Parkinson´s disease and dementia with Lewy bodies. This study is part of a larger effort aiming to expand the knowledge of brain-enriched proteins in human cerebrospinal fluid and to provide novel insight into the relation between such proteins and different neurodegenerative diseases.
The researchers report a multiplexed protein profiling using an affinity-based proteomics approach to generate cerebrospinal fluid profiles of brain-enriched proteins...Read more
Mitochondria are responsible for the energy production in our cells. The most interesting thing about mitochondria is that they have their own DNA which means some proteins in the mitochondria come from nuclear DNA and some from mitochondrial DNA. In a previous image of the week we highlighted TOMM5, a protein responsible for transport of nuclear encoded mitochondrial proteins into the mitochondria.
In this week's image of the week we take a look at citrate synthase (CS), a nuclear encoded mitochondrial protein that is a key enzyme for the citric acid cycle of the cell (TCA cycle), also known as the Krebs cycle...Read more
This week, it is Mitochondrial Disease Awareness Week. Therefore we would like to take the opportunity to talk about the mitochondrial proteome, the work we do within this field, and you will even get to meet one of our researchers, involved in this work.
The mitochondria are distributed throughout the cytoplasm of the cell, each organelle enclosed by a double membrane, the inner one forming the characteristic folds known as cristae. Mitochondria are essential for producing the cell´s need of ATP through cellular respiration, but have also been shown to participate in many other cellular functions, including apoptosis, calcium storage and cellular signaling...Read more
Welcome to another HPA image of the week! This week we take a look at another member of the vesicle family, the lysosomes.
In a way, lysosomes can be thought of as the recycling plants of your cells. Lysosomes are small membrane bound vesicular organelles that degrade biomolecules within your cells so that the materials in these molecules can be recycled and used for other cellular processes. Often these biomolecules come from vesicles known as endosomes that bring in materials from outside your cells, however lysosomes are also known to degrade other organelles, and products from within the cell...Read more
In an article in a special edition of Proteomics, on protein arrays researchers from the Human Protein Atlas describe the development of a novel assay concept, which combines the flexibility and multiplexing capacity of single-binder assays and the specificity and sensitivity aspects of dual-binder assays. They developed a multiplexed dual-binder assay procedure, which is based on a sequential protein capture.
– This assay is a great addition to the antibody-array toolbox of the Biobank Profiling Group, both to support related assay development activities and for biomarker discovery applications, says Burcu Ayoglu, first author of the study...Read more
This week's image of the week shows an example for the growing number of organelles that we annotate in the Cell Atlas. Lipid droplet (LD) proteins fall under the vesicle category, but starting with version 16, they will have their own place in the Atlas? organelle panel.
LDs can be found in animals, plants, fungi and even some bacteria have them. They have a simple and evolutionary conserved structure: A hydrophobic core that contains the lipids is surrounded by a phospholipid monolayer with proteins attached. This phospholipid monolayer makes the LDs unique among organelles; all other membranes consist of a double layer...Read more
An international working group has formulated directives to evaluate antibodies used in biomedical research. A paper in Nature Methods suggests five conceptual pillars for antibody validation.
Antibodies are used frequently both in research and in the clinic, and today over two million commercial antibodies are available for the analysis of human proteins. This has been accompanied with a dramatic development in clinical treatment of diseases, like cancer and autoimmune diseases, where biological drugs in the form of antibodies have changed the treatment of many patient categories...Read more
Welcome back blog fans! After a brief hiatus the image of the week highlights from the HPA are back! This week we are discussing the Endoplasmic reticulum, which is not just difficult to say, but is where many of your proteins are made.
The endoplasmic reticulum (ER) is one of the largest organelles in the cell. It is a delicate membranous network composed of sheets and tubules that spreads throughout the whole cytoplasm and is actually contiguous to the nuclear membrane. Two major forms of the ER can be distinguished: the rough ER and the smooth ER. Both have different functions...Read more
Adil Mardinoglu is a SciLifeLab fellow and the newest addition to the Protein Atlas team of principal investigators. He is the leader of the systems biology group, a group that create biological networks to identify drug targets and discover biomarkers for the development of efficient treatment strategies.
But Adil´s background is not in medicine, he is an electronic engineer with a PhD in computational biology.
– I did my PhD in Ireland where I worked with magnetic drug targeting, he says.
After a one year post doc doing research on neuronal networks, Adil Mardinoglu moved to Chalmers in Gothenburg to join Jens Nielsens group in systems biology...Read more
In a recent publication in Nucleic Acids Research, researchers from the Systems Biology group at the Human Protein Atlas investigated anomalies in regulation of lipid metabolism in the liver, in association with hepatocellular carcinoma.
Hepatocellular carcinoma has a high mortality rate and early detection of the disease is crucial for the application of effective treatment strategies. Several lines of evidence imply that lipid anomalies underlie the hepatocellular carcinoma pathogenesis.
Here, the researchers applied a tailored network-based approach to identify signaling hubs associated with regulation of this part of the metabolism...Read more
In a paper published in Nature Scientific Reports last week, researchers from the Human Protein Atlas describe a method for stratification of responders towards the drug eculizumab that allows for precision medicine and should be applicable to several other diseases and therapeutics.
The term precision medicine describes the idea of providing effective treatment based on a patient´s molecular make up. Recent advances in molecular diagnostic tools and handling of large data sets allow for the stratification of patients based on e.g. genetic or protein information and make it possible to provide tailored treatment for these sub-groups...Read more
This week, the image of the week highlights the Golgi apparatus. This week's contribution is brought to us by Peter Thul, a postdoctoral researcher who works on the Subcellular protein atlas, and specializes in understanding secretory pathway.
The Golgi apparatus was discovered by the Italian physician and scientist Camillo Golgi, who discovered the fine membraneous structure in 1898 (Mazzarello P., Garbarino C., & Calligaro A. 2009). Since then it has frequently drawn the attention of researcher because of its prominent role in the secretory pathway of cells.
The secretory pathway describes the route that proteins take to get to the outside of the cell...Read more
Though frequently overlooked as being a "catch-all" for proteins that don't reside within another organelle, cytoplasmic proteins are anything but.
One important role of proteins in the cytoplasm is the regulation of gene expression. There are two main ways in which gene expression is regulated; when converting the genetic code in your DNA to RNA (transcription), and when converting RNA to proteins (translation). Though transcription (DNA to RNA) occurs in the nucleus, cytoplasmic proteins are often involved in activating transcription factors which then move to the nucleus to perform transcription.
The protein stained in Fig 1...Read more
In a paper in a recent issue of Cell Metabolism, Human Protein Atlas-researchers investigate the biological processes that are altered in obese subjects.
Obesity is associated with an increased risk for a wide range of morbidities, including insulin resistance, type 2 diabetes, non-alcoholic fatty liver disease, and cardiovascular disease. Although the prevalence of obesity continues to dramatically increase worldwide, a clear understanding of the underlying molecular mechanisms involved in the progression of associated disorders is still lacking...Read more
In a recent number of Nature Reviews, Human Protein Atlas researchers Mathias Uhlén and Adil Mardinoglu discuss a study by E.G. Williams and co workers in Science where five complementary -omics datasets across various environmental states (including genomics, transcriptomics, proteomics, metabolomics and phenomics) using the liver as a platform for multiomics analysis are integrated...Read more
This week, image of the week highlights another organelle, the nucleoli fibrillar center!! This week's contribution is brought to us by Lovisa Åkesson, who works on the Subcellular protein atlas, and specializes in understanding nuclear function.
A few months ago, an excellent example of a protein located in the nucleoli rim was shown in another blog post. Today, we are diving deeper into the function of the nucleoli and specifically the fibrillar center, another nucleolar compartment.
As mentioned before, the nucleolus is a non-membrane bound structure located within the nucleus and there is usually more than one in each nucleus...Read more
Today we meet yet another researcher within the Human Protein Atlas project, Jochen Schwenk, Associate Professor for Translational Proteomics at KTH - Royal Institute of Technology in Stockholm, Sweden. He is Director of the Biobank Profiling facility at the Science for Life Laboratory and a Principal Investigator within the Human Protein Atlas and the KTH Center for Applied Proteomics.
– I have a PhD in Biochemistry from the University of Tübingen in Germany, and when I saw presentations from the Human Protein Atlas Director Mathias Uhlén at a few meetings I thought that this would be an exiting project to work with after my PhD thesis, Jochen Schwenk says...Read more
It's time for another HPA image of the week! This week we interrupt our series of organelle highlights to bring you another great image brought to us by the citizen scientists in Project Discovery, and specifically by x Truf a member of the Signal Cartel in EVE online who found this image while playing Project Discovery. This is x Truf's second contribution to our image of the week, and we'd like to give special thanks for these contributions!
The protein stained in Fig 1. is an image of Torsin A interacting protein 1 (TOR1AIP1, also known as LAP1). This staining shows signal specific to both the nuclear membrane and microtubules...Read more
In a recent publication in JCI Insight researchers from the Human Protein Atlas have described the expression of the currently known cancer-testis antigens (CTAs) in non-small cell lung cancer, and have added 50 new CTAs to this list.
Lung cancer is the most common cause of cancer related death in Sweden and worldwide. Most patient present with advanced disease and have a short life expectancy despite modern therapy.
Dijana Djureinovic is a PhD student in the group of Cecilia Lindskog at Science for Life Laboratory. She started her PhD studies two years ago, but worked in the project before that, on antibody validation...Read more
Let's have a look at another fascinating compartment of the cell, the centrosome! Located in close proximity to the nucleus, the centrosome is so small that it sometimes suffers from being overlooked. However, despite its humble size it is a very important organelle with great impact on cellular function.
The centrosome was first described in 1888 and has been a very popular organelle to study among biology researchers ever since (Conduit P.T. 2015). The most well characterized function of the centrosome is to serve as the organizing center for the microtubules that build up the internal architecture of the cell, the so-called cytoskeleton...Read more
Secreted and membrane-bound proteins are important for physiological processes and are potential drug targets as they are easily accessible in the extracellular space and provide a gateway to the intracellular environment. About 3,000 protein-coding genes are predicted members of the secretome; examples of secreted proteins are cytokines, coagulation factors, hormones, and growth factors. Important members of the membrane proteome, consisting of about 5,500 genes encoding predicted membrane-bound proteins, are ion channels of molecular transporters, enzymes, receptors, and anchors for other proteins.
A majority of the human genes encode several splice variants...Read more
It's time for another Image of the week! This week's image is brought to us by Diana Mahdessian, who works on the Subcellular protein atlas, and highlights cell division and various stages of mitosis. In previous blogs we have discussed the importance of certain proteins in the cell cycle including dividing centrosomes and FDXR in mitochondria.
The cell cycle is an ordered series of events that ultimately leads to the division of the "mother" cell into two "daughter" cells (cells are given feminine names because they are capable of reproducing).
The cell cycle consists of three distinct phases; interphase, mitosis and cytokinesis...Read more
A large number of proteins are needed in all cells throughout the human body. These proteins are sometimes called housekeeping proteins, suggesting that their expression is crucial for the maintenance of basic functionality of all normally functioning cells.
A transcriptomics analysis shows that about 9,000 genes are expressed in all tissues and are therefore expected to fulfill these tasks, such as gene expression, metabolism, and cell structure.
As for gene expression, it is easily understood that every cell must have proteins that are involved in the genetic machinery of translating DNA to functional proteins, like RNA polymerases and ribosomal proteins...Read more
Welcome back to HPA image of the week! This week we highlight another organelle brought to us by Mikaela Wiking aka HPA_Illuminator, the intermediate filaments!
Intermediate filaments are one of the three cytoskeletons of the cell, together with actin filaments and microtubules.
The expression of intermediate filaments can be extremely dependent on cell type, for example the intermediate filament protein group keratins, discussed in a previous IOTW, are key components in hair, nails and skin...Read more
In January 2015, the Tissue-based map of the human proteome by Uhlén 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
Welcome back to Image of The Week! We will be periodically highlighting an organelle in the coming image of the week posts, written by members of the Subcellular Human Protein Atlas project. This week we kick things off with a post by HPA_Illuminator, and what better way to start than with the mitochondria, the (true) powerhouse of the cell!!!
Mitochondria are found in almost all human cells, in varying numbers. They are known as the powerhouse of the cell as they are responsible for producing the majority of the energy in your body (in the form of ATP, adenosine triphosphate)...Read more
In a very recent study, published in Respiratory Research, researchers from the Human Protein Atlas and Karolinska Institutet performed protein profiling of broncho-alveolar lavage (BAL)-fluid and serum using an antibody suspension bead array technology with the aim to find proteins associated to sarcoidosis.
Sarcoidosis is a granulomatous systemic inflammatory disease in which more than 90 % of all patients develop pulmonary manifestations. Several gene associations have previously been described, but established and clinically useful biomarkers are still absent...Read more
Welcome to HPA image of the week! This week's image was brought to us by citizen scientists in Project Discovery, and specifically by solartech0 who found this image while playing Project Discovery in EVE online.
The protein stained in Fig 1. is an image of ferredoxin reductase (FDXR) found in the mitochondria of the cell. This sample shows a staining of FDXR in A549 adenocarcinomic alveolar basal epithelial cells.
FDXR is a protein involved in cellular metabolism. This process is what provides energy for our cells and is carried out in the mitochondria of the cell...Read more