PROTACs, PHOTACs and LYTACs: How to Target a Protein for Degradation

PROTACs for Targeted Protein Degradation
An illustration of PROTAC structure and the proteins it binds.

Targeting a single protein and making it disappear from the cell is quite the magic trick, and there are various molecular tools available for this task. You can use RNA interference, which prevents a protein from being made, inhibitors that bind the protein, rendering it unavailable for use or even gene editing tools like CRISPR that can remove it from the genome. But did you know that you can target an existing protein for destruction, using the cell’s own garbage disposal system to degrade the protein? All you need is a molecule that can connect your protein to one with a role in cellular protein degradation and your protein can be destroyed. Continue reading “PROTACs, PHOTACs and LYTACs: How to Target a Protein for Degradation”

Cancer is a Scourge Most Ancient

Reconstruction of Pappochelys rosinae or grandfather turtle. Attribution: Rainer Schoch [CC BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0)], via Wikimedia Commons
The first words that come to mind when people hear “Triassic” are likely dinosaur or maybe ginkgo or possibly even phytoplankton, but probably not cancer. For all that we have learned about how cancer develops based on the efforts of numerous research scientists, this disease is not solely a modern affliction. In fact, cancer has deep roots in the past. From several thousand year old human mummies to fossils millions of years old, cancer has left evidence of its presence in the historical record. Yes, even in the era of dinosaurs, cancer existed.

Cancer is usually a soft-tissue-based malady, but occasionally, it can also be found on bones, altering the bone’s surface and leaving unmistakable signs. Alterations like those observed on the femur of a 240-million-year-old shell-less stem-turtle found in modern-day Germany and described in JAMA Oncology. Continue reading “Cancer is a Scourge Most Ancient”

Cardboard Couture: From Conception to Runway Debut

The five-member team at the Read(y) To Wear event.

What do fashion, paperboard product packaging and literacy have in common? Answer: The Read(y) to Wear submission from a team of Promega employees for an event put on by the Madison Reading Project. With a challenge that stated teams need to make a garment mostly of paper, the resulting creations would be displayed on a runway as part of a charitable evening for an organization dedicated to bringing books to children.

Volunteering to be part of what became a five-person team to create a wearable garment from paper was the easy part. Our first few meetings we were experimenting with ideas and techniques using paper we could access on campus: Print catalogs, discarded books and our prototype product kit boxes. It was the kit boxes with the David Goodsell imagery that inspired our ideas to create a suit of armor. The paperboard boxes protect the products we ship to customers like a suit of armor protects warriors in battle. Continue reading “Cardboard Couture: From Conception to Runway Debut”

Expanding the Plague Family Tree: Yersinia pestis in the Neolithic

Yersinia pestis. See page for author [Public domain], via Wikimedia Commons

In recent years, scientists have been able to refine their molecular tools to resurrect ancient DNA from human graves and determine that yes, Yersinia pestis was the causative agent for the Black Death in the 14th century and the Plague of Justinian in the 6th century.  As more and more human graves have been uncovered, their DNA has revealed many secrets that scientists even ten years ago were unable to discover. With the ability to sequence entire genomes of bacteria that died with their hosts hundreds and even thousands of years ago, researchers are exploring the rise and possible spread of Y. pestis. Each new member sequence adds to the Y. pestis family tree, pinpointing the origin of this bacteria as it diverged from its ancestor Y. pseudotuberculosis. Peering into the past, scientists have been able to track down a strain of Y. pestis from individuals in a Swedish passage grave that is basal to known strains and that the authors of a Cell article suggest has interesting implications.

This pathogenic journey into history started by analyzing ancient DNA data sets from the teeth of individuals present in a communal passage grave in Gökhem parish, located in western Sweden, for any disease-causing microbial sequences that might be present. Y. pestis was flagged in one 20-year-old female dated 4,867–5,040 years ago. The bacterial sequences from this individual, named Gok2, were more closely aligned with Y. pestis than the Y. pseudotuberculosis reference genome. Continue reading “Expanding the Plague Family Tree: Yersinia pestis in the Neolithic”

How Prostate Cancer Cells Survive Glucose Deprivation

Illustration of energy metablism in cell.Glucose is an energy metabolite necessary for cellular survival and growth whether or not the cell is part of a tumor. Not only do cancer cells switch from oxidative phosphorylation to aerobic glycolysis (the Warburg effect) to gain more glucose, a hallmark of cancer, but they also increase the amount of glucose taken up from the surrounding extracellular space. However, the lack of glucose can have a negative effect on cells, causing them to become apoptotic in the absence of this metabolite. Cancer cells have methods to get around the requirement for glucose, including upregulating glucose transporters to improve access to the energy metabolite. In this Redox Biology article, researchers describe how activating androgen receptor in response to a lack of glucose affects the amount of GLUT1 expressed on prostate cancer cells, making the cells resistant to glucose deprivation.

To set the stage, two prostate cancer cell lines, LNCaP, an androgen-sensitive cell line, and LNCaP-R, an androgen-insensitive cell line, were deprived of glucose. Both cell lines showed signs of cell death, but LNCaP-R cells died in greater numbers. To probe how LNCaP cells died, several inhibitors (a pan-caspase inhibitor, two necroptosis inhibitors and a ferroptosis inhibitor) were added but did not change the way the cells died. However, an autophagy inhibitor enhanced cell death, suggesting the cells were necrotic not apoptotic. Teasing apart if the necrosis of LNCaP cells was due to glucose availability or merely disrupted glycolysis, the glucose analog 2DG was added to the medium with glucose. The cells survived when treated with 2DG, suggesting it was the absence of glucose that induced necrosis. When LNCaP cells were cultivated in medium that replaced glucose with mannose or fructose, the cells survived, another point in favor of sugar depletion causing cell death. Continue reading “How Prostate Cancer Cells Survive Glucose Deprivation”

Long-Lasting Beauty from the Humble Egg

“The Coronation of the Virgin” tempera on panel by Fra Angelico [Public domain], via Wikimedia Commons
Chicken eggs are widely found in most grocery stores. They are a cheap and unassuming source of protein, easy to cook as you desire (e.g., fried, scrambled, hard boiled) or use as a binder for other food items (e.g., meatloaf, cakes, cookies). One reason I keep laying hens myself is not only for fresh eggs but also to have egg shells other colors than white, the predominant color sold in US grocery stores. However, did you know that eggs have uses that don’t end up in the stomach and instead, are a feast for the eyes? I was introduced to the concept of egg tempera, a medium used for painting, by my colleague, Karen Stakun, artist and manager of our graphics department during a discussion about chickens. I was intrigued by the concept. Continue reading “Long-Lasting Beauty from the Humble Egg”

Finding Its Place: The Biohealth Industry in Wisconsin

On October 9, the 2018 Wisconsin Biohealth Summit was held in Madison, WI, hosted by BioForward, an organization that supports the growth of the biohealth industry in the state. This day-long event covered topics such as how diversifying your team can build better leadership, discovering new markets for existing products, and biomanufacturing. One of the panels on the schedule was “Examining the Economic Impact of Wisconsin’s Biohealth Industry,” and Penny Patterson, our Vice President of Communications, was one of the panel participants. We spoke after the summit to learn what came out of the panel discussion and the topics of interest raised by the biohealth industry attendees.

As we talked, Penny explained many topics were discussed, but ultimately focused around how to attract talented individuals to the biohealth industry in Wisconsin. This concern stemmed in part from the lower profile of the biohealth industry in Wisconsin compared to the more prominent and well-known East and West coasts. Of note, education and quality of life are important tools for recruiting candidates to join the biohealth industry. Continue reading “Finding Its Place: The Biohealth Industry in Wisconsin”

In Defense of Wild Spaces in the Yard

Pale purple asters and milkweed. Copyright S. Klink.
Surrounding my mowed lawn is a wild, mostly uncultivated space that currently has goldenrod blooming with tall asters starting to blossom. Every day when I pass these flowers, I see bumblebees, butterflies and other insects collecting the nectar to eat or store for the winter. Last year, when a section of soil was disturbed during construction of a building, I decided to seed the area with native wildflowers rather than grass. (I am not a fan of mowing the lawn.) Watching the series of flowers bloom over the late spring to autumn has been beautiful, colorful and full of tiny moments of joy. Not only do I see insects enjoying the flowering plants, but birds will land on the taller greenery, sometimes just resting, sometimes collecting seeds. I am not sure who has been startled more often, me or the birds when I walk by, flushing a bird from the thicket of tall plants.

Monarch butterfly on thistle photographed in the prairie at Promega headquarters in Madison, WI. Copyright Promega Corporation.
Where some people might see wild, unruly areas, I see Monarch butterflies on their daily flight, fluttering above me and the “weeds”. I have even been lucky enough to find Monarch caterpillars munching on milkweed, a common plant in my wild space. Despite my efforts, I have a lot of tall ragweed appearing in my yard, but have discovered that birds love the seeds, including my chickens, and squirrels will remove and eat the leaves. In addition, I see fireflies in early June through late August, many I find hanging out on the shady greenery during the day before their light display at night. Continue reading “In Defense of Wild Spaces in the Yard”

How Autophagy Feeds Cancer’s Need for Metabolites

Illustration of energy metablism in cell.Metabolism underpins numerous cellular processes. Without it, cells would not grow, divide, synthesize or secrete. Another pathway, autophagy, degrades unwanted cellular materials, helping to maintain cell health. With these opposing roles, is there a connection between autophagy and metabolism? As it turns out, the answer is yes. Because molecules degraded by autophagy are recycled and fed into metabolism pathways as precursor compounds. There are interesting implications as a result of this connection, ones that affect cancer cells as described in a recent Cell Metabolism review article.

Autophagic flux, the process by which molecules and organelles are directed to the autophagosome, fuse with the lysosome and are degraded, involves a selective process that determines the cargo carried within the autophagosome. Autophagy-related genes (ATGs) direct the process and particular receptor proteins bind the cargo. What is interesting about the connection among cancer, autophagy and metabolism is the complexity of the role that autophagy plays in cancer. While autophagy was thought to act in a more tumor suppressive manner as shown when one copy of an ATG6 analogous gene in mice was deleted and the other left unaltered, and malignant tumors developed, but in mice mosaic for ATG5 deletions, the inhibition of autophagy resulted in benign tumors in the liver. This latter experiment suggested autophagy was needed for cancer progression, a hypothesis reinforced by the lack of ATG mutations in human cancers. Continue reading “How Autophagy Feeds Cancer’s Need for Metabolites”

All You Need is a Tether: Improving Repair Efficiency for CRISPR-Cas9 Gene Editing

Ribonucleoprotein complex with Cas9, guide RNA and donor ssDNA. Copyright Promega Corporation.
With the advent of genome editing using CRISPR-Cas9, researchers have been excited by the possibilities of precisely placed edits in cellular DNA. Any double-stranded break in DNA like that induced by CRISPR-Cas9 is repaired by one of two pathways: Non-homologous end joining (NHEJ) or homology-directed repair (HDR). Using the NHEJ pathway results in short insertions or deletions (indels) at the break site, so the HDR pathway is preferred. However, the low efficiency of HDR recombination to insert exogenous sequences into the genome hampers its use. There have been many attempts at boosting HDR frequency, but the methods compromise cell growth and behave differently when used with various cell types and gene targets. The strategy employed by the authors of an article in Communications Biology tethered the DNA donor template to Cas9 complexed with the ribonucleoprotein and guide RNA, increasing the local concentration of the donor template at the break site and enhancing homology-directed repair. Continue reading “All You Need is a Tether: Improving Repair Efficiency for CRISPR-Cas9 Gene Editing”