Author: Michele Arduengo

Conversations: Nerve-Tumor Crosstalk in the Tumor Microenvironment

Posted on by Michele Arduengo
Cancer cells are characterized by features such as metabolic reprogramming and uncontrolled proliferation all of which are supported by underlying genomic instability, inflammation and the tumor microenvironment.

Cancer cells can be distinguished from normal cells by a variety of features including their ability to inappropriately activate signals for cell proliferation, evade growth suppression from contact inhibition or tumor suppressor activity, evade cell death signals, replicate DNA continually, induce angiogenesis, invade new tissues, reprogram their metabolism to provide energy for rapid proliferation, and evade immune detection (1) . Several biological processes are responsible for these features including genomic instability, inflammation, and the creation of a tumor microenvironment.

The tumor microenvironment is the network of non-malignant cells, connective tissue and blood vessels that surround and infiltrate the tumor. These surrounding “normal” cells interact with each other and the cancer cells and are important players in tumorigenesis. One cell type that is often found in the tumor microenvironment are nerve cells. In fact, cancer cells often express proteins that encourage nerve growth into the tumor microenvironment such as growth factors and axon-guidance molecules (2). Crosstalk between nerve cells and tumor cells can facilitate development of several cancer types (2) including pancreatic, head and neck, oral, prostate, and colorectal cancers.

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Avoid the Cloning Blues This Season

Posted on by Michele Arduengo

I was blasting a holiday music playlist while driving recently, and Presley’s Blue Christmas played. I couldn’t get the phrase “Christmas Cloning Blues” out of my mind, and by the time I arrived at my destination, this happened:

Cloning Blues Christmas

(to the tune of Blue Christmas by Elvis Presley)

Blue and white colonies on a selective plate. Careful planning can help you avoid the cloning blues
Blue/White cloning is a standard technique in molecular biology labs.

I’ll have a blue Christmas without you

Colonies so blue, insert without you

Incubating my plates at 37 degrees

Won’t be the same if you’re not in lacZ

And all those blue colonies are forming

When my lab mates’ clonings are performing

They’ll be doing alright,

With their plates all filled with white

But I’ll have a blue, blue, blue cloning

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A Virus Makes a Comeback: Emerging Poliovirus Transmission in the West

Posted on by Michele Arduengo

In 1921, at age 39, Franklin D. Roosevelt, the man who would later be elected the 32nd president of the United States, was diagnosed with polio (poliomyelitis). His symptoms included fever, gastrointestinal issues, numbness, and leg and facial paralysis. The disease left him paralyzed from the waist down, relying on a wheelchair and leg braces to walk.

The paralysis from poliovirus infection affected the involuntary muscles that allow breathing, and iron lungs were used to keep patients breathing until they cleared the infection.
The paralysis from poliovirus infection affected the involuntary muscles that allow breathing, and iron lungs were used to keep patients breathing until they cleared the infection.

At the height of the polio epidemic in 1952, more than 3,000 people died of polio in the United States, and 20,000 more people suffered paralysis. Pictures of the era show children in special hospital wards, inside ominous-looking iron lungs, while “recovered” children played on the grounds of hospitals wearing leg braces.

In 1938, Roosevelt founded the March of Dimes, which funded the development of the Salk polio vaccine. Two years after the introduction of the Salk vaccine in 1955, polio cases in the US dropped by 90%. In fact, sustained polio transmission has been absent from the US for nearly 40 years; according to the CDC, the last case of wild poliovirus in the US occurred in 1979.

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Keeping Cool When It Hurts: An Engineered Alternative to Pharmacological Pain Management

Posted on by Michele Arduengo

Pain management, particularly long-term pain management, is a difficult problem. Opioids are effective at reducing pain, but they are addictive and carry with them the significant costs of addiction and overdose that affect not only the individual but society as well. 

Saltatory conduction in neurons. Localized cooling of neurons may provide a non-addictive method for pain management.

Recently, work presented in Science by Reeder and colleagues proposes an engineering solution to pain management: miniature, implantable devices that can deliver localized and reversible neural blocking to reduce pain. While such devices could deliver any kind of stimulus ranging from electrical to pharmacological, the researchers developed a device that temporarily blocks neural signals by cooling.

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Designing Better Therapeutic mAbs: An Assay for Rapid, Parallel Screening of Fc/ FcɣR Interactions

Posted on by Michele Arduengo

The first monoclonal antibody (mAb) was produced in a lab 1975, and the first therapeutic mAb was introduced in the United States to prevent kidney transplant rejection in 1986. The first mAb used in cancer treatment the anti-CD20 mAb, rituximab, was used to treat non-Hodgkin’s lymphoma and chronic lymphocytic leukemia. Today therapeutic mAbs have become a mainstay of cancer, autoimmune disease, and metabolic disease therapies and include HERCEPTIN® used to treat certain forms of breast cancer, Prolia used to treat bone loss in post-menopausal women, and Stelara used to treat autoimmune diseases like psoriatic arthritis and severe Crohn disease, among many others. Therapeutic mAbs bind targets with high specificity and affinity and they can recruit effector cells to drive target elimination through mechanisms such as antibody-dependent cellular cytotoxicity (ADCC) or antibody-dependent cellular phagocytosis (ADCP), making them highly specific, effective therapies.

3D rendering of a Lumit Assay which can be used for plate-based screening assay to measure the affinities of Fc interactions of therapeutic mAbs.
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Use of ProAlanase Digestion Increases Number of Identified Methylglyoxal (MGO)-Modified Proteins in Whole-Cell Lysates

Posted on by Michele Arduengo
space filling structural model methylglyoxal (MGO)
Methylglyoxal is responsible for post translational protein modifications, that result in advanced glycation endproducts (AGEs), which are associated with aging and disease.

Post-translational modifications (PTM) of proteins are essential for the function of many proteins, but aberrant modification of protein residues also can interfere with protein function. PTMs occur in two ways. Proteins may be modified through the activity of enzymes such as kinases, phosphorylases, glycosylases and others that add or remove specific chemical moieties to amino acid residues. PTMs can also result from non-enzymatic reaction between electrophilic compounds and nucleophilic arginine and lysine residues within a protein. Metabolites and metabolic by products produced during glycolysis, especially glyoxal and methylglyoxal (MGO), are examples of such electrophilic compounds. These compounds can react with arginine and lysine to produce advanced glycation end products (AGEs), which are biomarkers associated with aging and degenerative diseases such as Alzheimer disease, diabetes and others. MGO is also elevated in tumors that have switched from oxidative phosphorylation to glycolysis as their main energy production pathway.

Only limited information is available about site-specific MGO PTMs in mammal cells, and most studies have focused on measuring the amount of MGO modifications in a treatment scenario compared to a control. Donnellan and colleagues recently published work to identify specific MGO protein modifications.  They used a “bottom-up” proteomic analysis of WIL2-NS B lymphoblastoid whole-cell lysates to identify specific MGO-modified proteins. In particular, the group was looking for modifications in proteins that might explain how MGO activity contributes to aneuploidy.

For the study, 100µg of cellular protein extract was reduced with dithiothreitol and then alkylated with chloroacetamide. The sample was diluted to reduce urea concentration. Trypsin Gold was added and samples were digested for 8 hours at 37°C. Digestion was terminated by adding formic acid. For ProAlanase digestion, 20µg of protein was reduced, alkylated and diluted to reduce urea concentration before adding digesting with ProAlanase for 4 hours at 37°C.

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The authors identified 519 MGO-modified proteins.  Most of the modifications were identified in the trypsin digestion reactions; however, ProAlanase digestion increased the number of MGO modifications identified by approximately 25% (with less than 4% of the modification sites being detected in both the ProAlanase and trypsin digestion reactions. The authors suggest that ProAlanase increased sequence coverage to reveal sites not detected in the trypsin digestions. Therefore, they conclude that ProAlanase can be used along with trypsin digestion to increase the identification of MGO modifications.

ProAlanase can be used along with trypsin digestion to increase the identification of MGO modifications.

MGO-modified proteins from the WIL2-NS whole cell lysates included proteins involved in glycolysis, translation initiation, protein folding, mRNA splicing, cell-to-cell adhesion, heat response, nucleosome assembly, protein SUMOylation and the G2/M cell cycle transition. More work to further characterize the sites of these modifications and their potential effects on the function of the modified proteins is ongoing.

Read more about ProAlanase, a new site-specific endoprotease from Promega.

Literature Cited

Donnelian, L et al. (2022) Proteomic Analysis of Methylglyoxal Modifications Reveals Susceptibility of Glycolytic Enzymes to Dicarbonyl Stress Int. J. Mol. Sci. 23(7), 3689 doi.org/10.3390/ijms23073689

PROTAC Virus Vaccines: A New Approach to Vaccine Development

Posted on by Michele Arduengo

Vaccine research and development is a major area of focus for life scientists across the globe. Clinical trials have shown that vaccines that target tumors show promise for cancer treatment. Additionally, the emergence of new zoonotic diseases has revealed a need to develop vaccines quickly as the world becomes more global and human populations interact more often with each other and wild habitats. Importantly, these vaccines need to be suitable for distribution in a variety of settings, including those that do not have easy access to refrigeration.

Influenza Virus. Si et al used influenza as a model to engineer and test PROTAC Virus vaccines

There are many ways to classify the different types of vaccines that are currently available. The National Institute of Allergy and Infectious Diseases in the United States, categorizes vaccines as: whole pathogen vaccines, subunit vaccines, and nucleic acid vaccines—based on how the antigen that stimulates the immune response is delivered to the host.

Whole-pathogen vaccines, which include many of vaccines used in clinical settings, use the entire pathogen (organism that causes the disease) that has been either weakened or killed to elicit a protective immune response. Killed vaccines are what their name implies: the pathogen has been killed so that it cannot cause disease, but enough of its structure remains to generate antibody response. Often, the immune response generated with killed vaccines is not as robust as that generated with other kinds of vaccines. 

Weakened or attenuated vaccines use whole pathogens that have been weakened in the laboratory through long-term culture or other means. Our modern MMR (measles, mumps and rubella) vaccine is an example of an attenuated vaccine. These vaccines tend to generate strong, long-lasting immune responses, but have increased risk for immunocompromised individuals.

Engineering an Influenza A PROTAC Virus Vaccine

A recent paper by Si et al published in Nature Biotechnology describes a new type of live-attenuated whole pathogen vaccine: the PROTAC virus. PROTAC viruses are prevented from replicating by targeting critical viral proteins for degradation using the host cell protein degradation pathway. The vaccine is live-attenuated by the host cells that degrade critical proteins.

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Detecting Disulfide Bond Shuffling in Biologics Using Trypsin Platinum

Posted on by Michele Arduengo
polypeptide chain showing protease cleavage sites
Learn about the new Trypsin Platinum Protease in this blog.

Biologic therapeutics such as monoclonal antibodies and biosimilars are complex proteins that are susceptible to post-translational modifications (PTMs). These chemical modifications can affect the performance and activity of the biologic, potentially resulting in decreased potency and increased immunogenicity. Such modifications include glycosylation, deamidation, oxidation and disulfide bond shuffling. These PTMs can be signs of protein degradation, manufacturing issues or improper storage. Several of these modifications are well characterized, and methods exist for detecting them during biologic manufacture. However, disulfide shuffling is not particularly well characterized for biologics, and no methods exist to easily detect and quantify disulfide bond shuffling in biologics.

Disulfide bond shuffling occurs when the S-S linkage is not between a Cys and its normal partner
Disulfide bonds are important for protein conformation and function

Normally the cysteines in a protein will pair with a predictable or “normal” partner residue either within a polypeptide chain or between two polypeptide chains when they form disulfide bonds. These normal disulfide bonds are important for final protein conformation and stability. Indeed, disulfide bonds are considered an important quality indicator for biologics.

In a recently published study, Coghlan and colleagues designed a semi-automated method for characterizing disulfide bond shuffling on two IgG1 biologics: rituximab (originator drug Rituxan® and biosimilar Acellbia®) and bevacizumab (originator Avastin® and biosimilar Avegra®).

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World Art Day: Experiences of Fine Art That Disrupt and Drive Innovation

Posted on by Michele Arduengo
This metal sculpture adorns the parking garage that serves Promega Kornberg and Feynman buildings on the Madison, WI, USA campus.
This metal sculpture adorns the parking garage that serves Promega Kornberg and Feynman buildings on the Madison, WI, USA campus.

World Art Day embraces art as a means for nurturing creativity and innovation, gaining greater understanding of cultural experiences that are different from our own, and showcasing the contributions of art and artists to sustainable development. It is no accident that World Art Day is celebrated on the birthday of Leonardo da Vinci, the celebrated Italian polymath who used art to express emotions, articulate technological concepts well before their time, and understand the workings of human anatomy.

Takaski Mitachi, a moderator of the 2019 global conference panel on Innovation through Art: Leveraging Disruption for a Sustainable Ecosystem, said that “Art can add value so that we could drive innovation beyond logic and data.” In a sense, the fine arts are a way of expressing our observations about the world around us, similar to how an original scientific hypothesis attempts to explain phenomena we observe and want to test. While scientific investigation builds on data and logic to test a hypothesis, art gives us a different way of knowing our world that extends beyond just data and logic. When we explore the arts, we broaden our understanding and interpretation of the world and bring these new perspectives to our scientific and technological explorations. Art is a disruptor of staid ways of thinking about and approaching problems, and like many other disruptors in our world, it can drive innovation.

In an article in the MIT Technology Review, author Sarah Lewis discusses the relationship between the arts and scientific breakthroughs. She notes one study that found a disproportionately high number of Nobel Prize-winning scientists also pursue art, writing or music as serious avocations. When asked why achievement in art and science seem to go together, she replied: “What the arts allow us to do is develop the muscle required for discernment and also strengthen our sense of agency to determine for ourselves how we’re going to tackle a given problem…Ultimately it’s up to the person creating the work to determine what that path is, and that kind of agency is what’s required for innovation.”

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Using Structural Computation Models to Predict Productive PROTAC Ternary Complexes

Posted on by Michele Arduengo

With use and time things wear out. Tires get worn on a car, and you have the old tires removed, recycled, and replaced with new ones. Sometimes a part or piece of something isn’t made properly. For instance, if you are assembling a piece of furniture and you find a screw with no threads, you throw it out and get a screw that was made properly. The same thing holds true for cells. Components wear out (like tires) or get improperly made (a screw with no threads), or they simply have a limited lifetime so that they are available in the cell only when needed. These used and worn components need to be removed from the cell. One system that allows cells to recycle components and remove old or improperly functioning proteins is the Ubiquitin-Proteasome System (UPS).  The UPS system relies on a series of small peptide tags, ubiquitin, to mark a protein for degradation. Researchers are now harnessing the UPS to target aberrant proteins in diseased cells through PROteolysis TArgeting Chimeras or PROTACs. PROTACs hold promise as highly efficacious therapeutics that can be directed to eliminate only a single protein. To take full advantage of the power of PROTACs, researchers need to understand the molecular underpinnings that are responsible for successful protein degradation. Here we review a paper that seeks to develop a computer model for predicting whether PROTAC ternary complex formation leads to ubiquitination and successful degradation of a target protein.

Diagram of ubiquitination of a protein. ThePROTAC ternary complex is formed the E2/E3 complex, PROTAC and target protein are bound simultaneously
Proteins are targeted for degradation by the proteasome. A small chain of ubiquitin peptides (Ub) is added to available lysine residues of the target protein through the actions of three enzymes: E1, ubiquitin-activating enzyme; E2, ubiquitin-conjugating enzyme; and E3 ubiquitin ligase. After the addition of the Ub chain, the proteasome is recruited and the protein degraded.

Addressing the Intractable Target

Research to understand diseases including cancers, neurodegeneration, and auto-immune conditions has revealed that in many disease states, affected cells produce growth factors or enzymes that are constitutively active (“always on”). These proteins are targets for small molecule inhibitors that bind specific sites preventing the constitutive activity or signaling. More recently, biologics, or protein-based therapeutics, including monoclonal antibodies (mAb), have been developed that can bind and block inappropriate signaling pathways, especially those that allow cancer cells to escape immune system surveillance.

Unfortunately, up to 85% of targets have proven intractable to small molecule inhibitors, or they are not suitable for a biologics approach. Oftentimes, the target protein doesn’t have a great place to bind a small molecule, so even though inhibitors might exist they cannot bind well enough to be effective. Or, as in the case of many cancers, the diseased cell manages to overcome the effect of the inhibitor by overexpressing the target. Still other aberrant proteins associated with diseases haven’t gained function to cause a disease; they have instead, lost function, so designing an inhibitor of the protein is not a workable strategy.  Enter the PROTAC.

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