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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Welcome to another HPA image of the week! This week we take a look at vesicles and another type of data present in the HPA.
The protein stained in Fig 1. is an image of RAB5C. This protein is found in vesicles and specifically, in lysosomes of the cell. This sample shows HeLa human cervical adenocarcinoma cells.
These cells are actually transgenic and made to express green fluorescent protein on the RAB5C protein (RAB5Cgfp). This is a method we use to check the validity of our antibodies...Read more
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
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
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