Illuminating the Function of a Dark Kinase (DCLK1) with a Selective Chemical Probe

The understudied kinome represents a major challenge as well as an exciting opportunity in drug discovery. A team of researchers lead by Nathanael Gray at the Dana Farber Cancer Institute was able to partially elucidate the function of an understudied kinase, Doublecortin-like kinase 1 (DCLK1), in pancreatic ductal adenocarcinoma cells (PDAC). The characterization of DCLK1 in PDAC was realized by developing a highly specific chemical probe (1). Promega NanoBRET™ Target Engagement (TE) technology enabled intracellular characterization of this chemical probe.

The Dark Kinome

NanoBRET target engagement

Comprised of over 500 proteins, the human kinome is among the broadest class of enzymes in humans and is rife with targets for small molecule therapeutics. Indeed, to date, over 50 small molecule kinase inhibitors have achieved FDA approval for use in treating cancer and inflammatory diseases, with nearly 200 kinase inhibitors in various stages of clinical evaluation (2). Moreover, broad genomic screening efforts have implicated the involvement of a large fraction of kinases in human pathologies (3). Despite such advancements, our knowledge of the kinome is limited to only a fraction of its family members (3,4). For example, currently less than 20% of human kinases are being targeted with drugs in clinical trials. Moreover, only a subset of kinases historically has garnered substantial citations in academic research journals (4). As a result, a large proportion of the human kinome lacks functional annotation; as such, these understudied or “dark” kinases remain elusive to therapeutic intervention (4).

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RiboMAX and the Effort to Find Antiviral Drugs to Fight Coronaviruses and Enteroviruses

Prior to 2020, there were two major outbreaks of coronaviruses. In 2003, an outbreak of SARS-CoV sickened 8098 people and killed 774. In 2012, an outbreak of MERS-CoV began which so far has sickened 2553 and killed 876. Although the overall number of MERS cases is low, the disease has a high fatality rate, and new cases are still being reported. Even though fatality rates are high for these two outbreaks, containment was quickly achieved. This makes development of a treatment not commercially viable so no one had undertaken a large effort to develop an approved treatment for either coronavirus infection.

Fast forward to late 2019/2020… well, you know what has happened. There is currently no reliable antiviral treatment for SARS-CoV-2, the coronavirus that causes COVID-19 infections.

Zhang, et al. thought of a way to make an antiviral treatment commercially viable. If the treatment is actually a broad-spectrum antiviral, it could be used to treat more than one infection, meaning, it can be used to treat more people and thus be seen as more valuable and worth the financial risk to pharmaceutical companies. So, they decided to look at the similarities between coronaviruses and enteroviruses.

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Public-Private Initiative to Increase COVID-19 Testing Capacity by Using Promega Maxwell Instrument in India

This blog is written by guest blogger, Dr Rajnish Bharti, General Manager of Promega Biotech India Pvt Ltd.

As COVID-19 cases accelerate, the country of India has decided to scale up testing capacity to 100,000 tests per day in the coming days.

In a major step to counter the coronavirus crisis, Promega India is supporting government agencies through our automated instruments. The Maxwell® RSC instrument is a compact, automated RNA extraction platform that processes up to 48 samples simultaneously in less than 35 minutes. The automated Promega solution allows laboratories to process up to 400 samples in a typical 8-hour shift.

Scientists in India train on the Maxwell RSC 48
Forensic Science Laboratory-Jaipur and SMS Hospital Jaipur join hands together to use Promega Maxwell® RSC 48 to Increase COVID-19 Testing capacity.
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A Valuable AP Biology Throwback

Today’s blog is written by guest blogger, Isobel Utschig, a science teacher at Dominican High School in Whitefish Bay, WI. We bring this to you in celebration of #TeacherAppreciationWeek 2020

About 10 years ago, I attended a field trip at the Biopharmaceutical Technology Center Institute with my AP Biology classmates. I felt apprehensive upon seeing the micropipettes and other “foreign” lab supplies on the benchtops. We learned that we would be using enzymes to cut DNA and visualize those different fragments on a gel. I marveled at the glowing streaks and found it incredible that I was looking (albeit indirectly) at real pieces of DNA. As we moved into the genetic transformation activity I was even more intrigued. We opened the tubes of bacteria and added some luciferase DNA, which would allow the bacteria to create a light-producing protein.  We then “heat shocked” the bacteria to coax them to take up these plasmids from their environment looking at the bacteria later, their glow revealed our success. The day flew by and at the end I marveled at all that we had done!

Students from Dominican High School AP Biology busy at work 
during a BTC Institute field trip
Students from Dominican High School AP Biology busy at work
during a BTC Institute field trip

Three years later I joined a research lab at Marquette University. Upon seeing the lab benches full of unfamiliar equipment, the same wave of apprehension came over me. My PI introduced me to the first task: digest a plasmid with restriction enzymes and verify the cut with gel electrophoresis. Memories of the high school field trip flooded my mind as I gripped a micropipette and attempted to nimbly load the wells. While I greatly improved in my skills over the course of the summer, the familiarity I had from my trip to the BTC Institute put me at ease from the beginning.  

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Skype a Scientist While You Stay at Home

A few weeks into Wisconsin’s Safer at Home order, I saw a tweet from Sarah McAnulty, PhD, the founder and Executive Director of Skype a Scientist, proclaiming that the organization was making a big change in response to the COVID-19 pandemic—they were allowing groups smaller than five people to sign up, meaning that families stuck at home during the pandemic could meet a scientist virtually in their living room.

Skype a Scientist provides an easy way to for people to meet a scientist and allows scientists to reach people from all over the world without having to leave the lab. Teachers (and now families) can choose the type of scientist that is a good fit, from computer scientists to marine biologists and everything in between. You can also request a scientist from a group that is underrepresented in STEM fields so that participants can see a scientist who looks like them or can relate to their experiences.

I learned about Skype a Scientist a few years ago after listening to an episode of the HelloPhD podcast. I remember wishing this program had existed when I was a high school science teacher, so I was ecstatic to learn it was now possible to participate and immediately filled out the online application for our family to be matched with a scientist. We received our match the next day and scheduled a call with our scientist the following week.

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NanoLuc® Luciferase Powers More than Reporter Assays

Bright NanoLuc® Luciferase

NanoLuc® luciferase has been discussed many times on this blog and our web site because the enzyme is integral to studying genetic responses and protein dynamics. While NanoLuc® luciferase was first introduced as a reporter enzyme to assess promoter activity, its capabilities have expanded far beyond a genetic reporter, creating tools used to study endogeneous protein interactions, target engagement, protein degradation and more. So where did the NanoLuc® luciferase come from and how does a one enzyme power several technologies?

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Targeting IL-6: How A Drug That Helped a 6-Year-Old Beat Cancer Can Save COVID-19 Patients

In 2012, a 6-year-old girl named Emily Whitehead was battling acute lymphoblastic leukemia (ALL), one of the most common cancers in children. Her cancer was stubborn. After 16 months of chemotherapy, the cancer still would not go into remission. There was nothing else the doctors could do, and she was sent home. She was expected to survive only a few more months. Her parents would not give up and enrolled her into a clinical trial of a new immunotherapy treatment called chimeric antigen receptor (CAR) T cell therapy. She was the first pediatric patient in the program.

Doctors took T cells from Emily’s blood and reprogrammed them in a lab. They essentially sent her T cells to boot camp where they are trained to find cancer cells and destroy them. The reprogrammed T cells were then injected back into her body. A week into treatment, she started getting a fever, the first sign that the treatment was working and her reprogrammed T cells were fighting the cancer. But soon, she got very sick. All of the indicators suggested that she had cytokine release syndrome (CRS)—also known as the cytokine storm. This happens when cytokines are released in response to an infection but the process cannot be turned off. The cytokines continue to attract immune cells to the infection site, causing damage to the patient’s own cells and eventually resulting in acute respiratory distress syndrome (ARDS). (Learn more about the cytokine storm in this blog.)

Emily was soon on a ventilator. Tests showed that she had extremely high levels of one particular cytokine: interleukin-6 (IL-6). Desperate to keep her alive, her doctors gave her a known drug that specifically targets IL-6. The results were dramatic. After one single dose, her fever subsided within hours, and she was taken off the ventilator. On May 2nd, 2012, she woke up from an induced coma—it was her 7th birthday. Her doctors said they have never seen a patient that sick get better that quickly.

The drug that saved her life was tocilizumab.

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Adapting Our Projects, Our Experiments, and Ourselves to Support COVID-19 Response

The COVID-19 pandemic has affected virtually everyone’s lives and business, and Promega is no exception. If you’re a frequent reader of Promega Connections, you have probably noticed that many of our recent blog posts have mentioned the novel coronavirus.

Madison Scientific Applications Team working on projects before physical distancing.

As Applications Scientists at Promega, we have adapted our work to enable support of our Promega colleagues and their customers as they respond to the pandemic. Like other groups in the company, we have ramped up our efforts. Our team typically has a broad focus on a variety of projects from across market segments of the company. During the second week of March, we switched to completely focus on virus-related experiments. Everyone on our team was in the lab collaborating on a large project to determine which kits could be used to purify viral nucleic acid from universal transport medium for virus (UTM®) and sputum, knowing that customers would be using any kit that they had on hand to do testing quickly. We completed testing in two days and data analysis and write-up within another couple of days.

In the last six weeks, we have worked on over 30 projects and completed almost 20 of them. In some cases, we identified, resourced, and began projects in the same day. In other cases, we completed projects within a day or two of receiving the request. You can find some of our data, presented as “Viral RNA Extraction Application Notes”, here.

Many projects originated from direct questions from global branches, Technical Services, and other internal colleagues on behalf of their customers. Some projects resulted from a need we identified, such as testing alternative storage methods for swab transport due to shortage of UTM®. Projects ranged from testing purification kits with relevant sample types, to comparing amplification reagents, and participating in work on forthcoming virus-related products.

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Getting a PhD in Sweatpants: Guest Blog by Dr. Susanna Harris

Today’s blog is guest-written by Susanna Harris, who recently defended her PhD thesis at the University of North Carolina in Chapel Hill.


I just defended my PhD. Nearly six years of blood, sweat, and tears, most of which were cleaned up with Kimwipes while sitting at my desk in a laboratory facing out towards the UNC Chapel Hill football field. Nearly six years of work, all summed up in a handful of slides. Nearly six years of work, explained to my friends, family, and colleagues – a moment I had dreamed of since the fall of 2014.

What I hadn’t dreamed of? That I would be sitting at my small desk in the corner of my room, with no present audience aside from my snoring dogs. That there would be no dinner celebration that carried into a night of fun along Franklin Street. That, unseen by the viewers of my defense, I would be wearing sweatpants as my name changed from Ms. to Dr. Harris.

Pictured: The audience for Susanna’s thesis defense.

Why did I wear sweatpants when I could have worn literally anything in my closet? Because I think it’s hilarious. I believe this situation will end and we will walk away with memories and lessons learned from an extremely difficult time in the history of the world. I want to walk away with one more ridiculous story to add to a long list of “What even was that?” tales from grad school.

Working towards a PhD is hard at any time; let’s not pretend this pandemic isn’t making things even worse. I was fortunate in many ways that my advisor had already moved our laboratory to a new state in 2019, allowing me to adjust to meeting through webcams and working from home before the pandemic changed the lives of all North Carolinians. This has given me a unique perspective to tease out which problems come from distance working and which are the result of Safer-At-Home orders. Based on my experiences, here are a few tips, tricks, and words of warning.

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