Regeneration Powers Activated! Regrowing the Liver from Stem Cells

“Form of rhino! Form of tidal wave!” The Wonder Twins from the TV show, Super Friends, fascinated me as a small child. With a simple uttered phrase the twins could transform into a rhino surfing a tidal wave. The hitch to their power was that it took both to transform. The adult science me finds this fact very reminiscent of stem cells that rely on communications from neighboring cells to transform into a specific cell type.

What is the power phrase uttered to adjacent stem cells? Do the cells require physical contact like the Wonder Twins to transform? To answer these questions, Asai and colleagues investigated the requirements for stem cells to transform into the form of a liver (Asai et al., 2017). They tested if the cells had to contact one another to initiate transformation, the key requirement for the Wonder Twins. In a special chamber, the group placed different types of stem cells. They found that while the stem cells could differentiate into liver cells, they could not fully form a liver-like structure unless they touched. To understand the power phrases uttered by stem cells, Asai and colleagues used the SOMAscan assay to tease out the communications between stem cells and their neighbors to transform into a liver. They found that the power phrases, which consisted of protein signals, changed depending on which types of cells were present.

This work is a large step forward in understanding the mechanisms employed by the body to regenerate the liver. These insights will no doubt will be invaluable to the research and medical community who seek to understand the secrets of the Wonder Stem Cells.

References

Asai, A., Aihara, E., Watson, C., Mourya, R., Mizuochi, T., Shivakumar, P., . . . Bezerra, J. A. (2017). Paracrine signals regulate human liver organoid maturation from induced pluripotent stem cells. Development, 144(6), 1056-1064. doi:10.1242/dev.142794

Moving Beyond Potential

Gripping a steering wheel sheathed in supple leather and driving down a winding road in a luxury car with ultra-responsive handling and superb performance… What could be more fun or exhilarating? Now, imagine if we swapped out the engine with a hamster and its wheel. The very same drive would not be as fun. Clearly, what goes on under the hood of the car is as important as the shining exterior and trimmings.

The SOMAscan® assay, like a fine luxury car, relies upon superb components to provide the customer with what they want—accurate measurement of relative protein levels in a biological sample. SomaLogic scientists finely craft each of these components, known as SOMAmers® (Slow Off-rate Modified Aptamer), to bind a specific target protein. The quality of each SOMAmer is rigorously assessed to ensure that it binds its target, and thus gives each customer exquisite data.

To check the specificity, each SOMAmer is tested for cross-reactivity with commercially available proteins that are similar to the original target. Scientists assess the strength of any off-target interactions, and if possible gauge the SOMAmer’s capabilities of engaging its target in plasma.

As is true of all high-performance vehicles, occasionally a flaw arises. If a SOMAmer binds strongly both to the original target and to very similar proteins, a redesign of the SOMAmer is initiated. After the SOMAmer engineers give the go ahead, the new SOMAmer is added to the next version of the SOMAscan assay.

Recently the SOMAmer engineers evaluated the entire SOMAmer fleet in the current SOMAscan assay. They observed that the vast majority of the SOMAmers bound specifically to their target. Also, a small fraction of the SOMAmers bound to  related proteins with a similar affinity to the original target protein or weakly. Complete information is available in a newly released White Paper.

SomaLogic is committed to ensuring the accuracy of its core technology by giving unequalled attention to the design, quality and performance of the SOMAmer reagents at the heart of the SOMAscan assay. Knowing the quality of the components under the hood gives us great confidence in where the whole vehicle takes us.

Hot Proteins: Intrinsically Disordered Proteins – A True Source of Super Powers

Mutant spider bites, exposure to radiation, freakish lab accidents, huge sums of wealth or just innate abilities give rise to figures that young and old adore. Super heroes! Their stories can sound just as fantastic as their powers. What if I were to tell you that some fantastic powers are real and transferable? Would you believe me?

On a third planet revolving about a yellow sun resides a being possessing the ultimate defenses. This entity has been hurled into the vacuum of space or abandoned in the driest of places only to survive (Boothby et al., 2017; Jonsson, Rabbow, Schill, Harms-Ringdahl, & Rettberg, 2008). No matter what the “evil” scientists can think of the “hero” thwarts their attempts and survives. Who is this remarkable protagonist? It is the lowly water bear (a.k.a. Tardigrades).

Poked and prodded for centuries, the mighty water bear finally revealed a source of its power to a team of scientists (Boothby et al., 2017). The secret lay within the water bear’s tardigrade-specific intrinsically disordered proteins, which lack a rigid structure and resemble spaghetti. Upon the water bear’s exposure to dry conditions, these proteins weave around things within the cells, essentially freezing everything in place. This act places the water bear in a suspended animation-like state. The water bear can survive in this state for years if not decades, until favorable conditions present themselves.

With the source of the power identified, the scientists transferred the formidable water bear’s power (i.e., they inserted the gene) into their usual lab minions, yeast and bacteria. The transfer was successful: The bacteria and yeast recipients could now withstand the harsh dry conditions too.

Not as exciting as lasers coming out eyeballs or leaping tall buildings in a single bound, the water bear’s transferable superpower still holds potential for helping mankind (Boothby et al., 2017). For example, the technology could help feed the masses through the engineering of drought-tolerant crops. It could also prolong the shelf-life of life-saving medicines and research supplies.

Only one more question remains regarding the superhero water bear: What would its costume look like?

References

Boothby, T. C., Tapia, H., Brozena, A. H., Piszkiewicz, S., Smith, A. E., Giovannini, I., . . . Goldstein, B. (2017). Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation. Mol Cell, 65(6), 975-984 e975. doi:10.1016/j.molcel.2017.02.018

Jonsson, K. I., Rabbow, E., Schill, R. O., Harms-Ringdahl, M., & Rettberg, P. (2008). Tardigrades survive exposure to space in low Earth orbit. Curr Biol, 18(17), R729-R731. doi:10.1016/j.cub.2008.06.048

Goodbye Poke, Hello Pee: Alternatives to Plasma for Heart Disease Diagnosis

I admit it: The sight of needles gives me the shivers. The moment the doc requests a blood sample, I want to hightail it to the next state over. And I am not alone in this viewpoint. Many people despise needles. This apprehension can be bad enough that people forgo medical treatment just to avoid the poke.

How nice would it be if lab samples could be collected without involving pain? Happily, this idea is becoming a reality.

Researchers at SomaLogic and the University of California San Francisco have sought to minimize the use of the dreaded needles by utilizing urine instead of plasma to assess heart health (Hraha et al., 2016). When arteries start to harden (arteriosclerosis), changes occur throughout the body, even in kidneys. And certain changes in the kidneys could potentially be observed through fluctuations in protein signatures in urine.

With access to urine and plasma samples from people with stable coronary heart disease, the researchers began their quest. To identify potential biomarkers, they used a version of the SOMAscan® assay that measured 4316 protein concentrations simultaneously. These measurements were compiled with the patients’ medical histories to yield a panel of markers that could predict an oncoming cardiovascular event. The panel performance for urine samples was comparable to a panel developed for plasma, which itself already performed better than standard prediction methods (Ganz et al., 2016).

Jubilation! It is foreseeable that urine collection can replace blood collection in the near future, helping ease people’s minds. It may make them more inclined to go to the doc and not forgo medical treatment.

References

Ganz, P., Heidecker, B., Hveem, K., Jonasson, C., Kato, S., Segal, M. R., . . . Williams, S. A. (2016). Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients With Stable Coronary Heart Disease. JAMA, 315(23), 2532-2541. doi:10.1001/jama.2016.5951

Hraha, T., DeLisle R., Ash, J., Ostroff R., Williams S., Ganz P. (2016, November). Urinary Proteome and Its Application to Predict Cardiovascular Risk in Patients with Stable Coronary Heart Disease. Poster session presented at American Heart Association Scientific Sessions, New Orleans, LA.

When to Trust Reagents: Gotta Have Faith… or Do We?

Have you experienced the following scenario? You are at a rock concert (or a team-building exercise at work) and lean back into a mosh pit (or group of your co-workers) with the expectation that they will catch you. If you have faith in people, then you would probably lean back and fall. If they catch you, great. If they let you fall, then an enormous “ouch” awaits you.

In research, many times we exercise a blind trust with our reagents and too often experience a huge ouch due to a lack of validation. Sometimes, the ouch can be tolerable. Other times, it truly is a matter of life or death.

Strict quality control is crucial for the development of safe and potent vaccines. A failed vaccination opens the door for the recipient to develop the disease and potentially die, even though the person thinks he or she is immune. Pharmaceutical companies realize this possibility and take great care to ensure the vaccines will work every time, year after year. Antibodies are needed to test vaccine potency, but antibody performance can be questionable at times. Recently, Merck began to explore alternatives to antibodies.

In Merck’s investigation of antibody alternatives, it assessed SomaLogic’s SOMAmer® reagents (Trausch, Shank-Retzlaff, & Verch, 2017). Thanks in part to SomaLogic’s proprietary technology, SOMAmers exhibit the same tight specific interaction with their target proteins as is observed in high quality antibodies. However, unlike antibodies, SOMAmers are made synthetically. This reduces the batch-to-batch variability, increases purity, speeds development, and reduces cost.

The Merck scientists conducting the work remarked on the virtues of the SOMAmers. They noted that SomaLogic delivered SOMAmers possessing the desired specificity. In the vaccine potency assay, the SOMAmers performed well. The use of the SOMAmers allowed the scientists to develop a new version of the assay that required fewer materials, fewer steps and required less time.

As trust in antibodies can falter, it’s good to know that reliable alternatives exist. Ready to lean back?

Reference

Trausch, J. J., Shank-Retzlaff, M., & Verch, T. (2017). Development and Characterization of an HPV Type-16 Specific Modified DNA Aptamer for the Improvement of Potency Assays. Anal Chem, 89(6), 3554-3561. doi:10.1021/acs.analchem.6b04852

I Got You: The Strong Bond Between a SOMAmer and Its Protein

What thoughts give you a warm fuzzy feeling? A basket of golden retriever puppies or wriggly mewing kittens? Maybe loved ones or friends? We humans evolved to be social creatures. Without a social network, we could potentially face a lonely existence that wreaks havoc on our mental and physical health (Perissinotto, Stijacic Cenzer, & Covinsky, 2012). We are not alone in our need of social contact: Many creatures from the humble bee to the giants of the sea need connections to thrive.

In a sense, one can imagine that the tiny nucleic acids called “aptamers” are also “evolved” to share a strong connection with a target, such as proteins. The modified aptamers (SOMAmers®), created out of SomaLogic’s proprietary technology, share some of the strongest bonds with their partners that are difficult to break on their own.

In a recent review, researchers at SomaLogic analyzed the binding interaction of SOMAmers with their targets and compared them to the ones shared between unmodified aptamers and their targets (Gelinas, Davies, & Janjic, 2016). The analysis revealed that the SOMAmer’s unique modifications are critical to the strength of the binding event. This type of binding tends to be stronger than interactions between aptamer and protein, which involve base stacking (an arrangement of nucleic acid bases and amino acids that resembles a stack of pancakes), hydrogen bonding, and electrostatic interactions (positively charged molecules binding to negatively charged molecules). The strong interaction shared between a SOMAmer and its target is more reminiscent of the interaction between antibodies and their proteins than of DNA-protein interactions.

Aside from analyzing the binding interactions, the researchers also compared the structures of both aptamers and SOMAmers. In their analysis, they observed that both aptamers and SOMAmers shared some structural elements that are abundant in the nucleic acid structure field. With their modifications, however, SOMAmers go on to adopt many new and novel structures.  It is increasingly clear that SOMAmer modifications provide the glue that can both hold the SOMAmer together and drive the strong bond with its specific target protein partner.

References

Gelinas, A. D., Davies, D. R., & Janjic, N. (2016). Embracing proteins: structural themes in aptamer-protein complexes. Curr Opin Struct Biol, 36, 122-132. doi:10.1016/j.sbi.2016.01.009

Perissinotto, C. M., Stijacic Cenzer, I., & Covinsky, K. E. (2012). Loneliness in older persons: a predictor of functional decline and death. Arch Intern Med, 172(14), 1078-1083. doi:10.1001/archinternmed.2012.1993