Repair Gone Wrong: Targeting The DNA Damage Response To Treat Cancer

By Gesa Junge, PhD

 

Our cells are subject to damage every minute of every day, be it from endogenous factors such as reactive oxygen species generated as part of normal cell respiration, or exogenous factors such as UV radiation from the sun. Together, these factors can lead to as many as 60 000 damaged DNA bases per cell per day. Most of these are changes to the DNA bases or single strand breaks (SSBs), which only affect one strand of the double helix, and can usually be repaired before the DNA is replicated and the cell divides. However, about 1% of SSBs escape and become double stand breaks (DSBs) upon DNA replication. DSBs are highly toxic, and a single DSB can be lethal to a cell if not repaired.

Usually, cells are well-equipped to deal with DNA damage and have several pathways that can remove damaged DNA bases and restore the DNA sequence. Nucleotide excision repair (NER, e.g. for UV damage) and base excision repair (BER, for oxidative damage) are the main SSB repair pathways, and homologous recombination (HR) and non-homologous enjoining (NHEJ) repair most DSBs. HR is the more accurate pathways for DSB repair, as it relies on a homologous DNA sequence on the sister chromosome to restore the damaged bases, whereas NHEJ simply relegates the ends of the break, potentially losing genetic information. However, NHEJ can function at any time in the cell cycle whereas HR requires a template and is only active once the DNA is replicated (i.e. in G2 and S-phase).

Depending on the severity of the damage, cells can either stop the cell cycle to allow for repair to take place or, if the damage is too severe, undergo apoptosis and die, which in a multicellular organism is generally favourable to surviving with damaged DNA. If cells are allowed to replicate with unrepaired DNA damage, they pass this damage on to their daughter cells in mitosis, and mutations in the DNA accumulate. While mutations are essential to evolution, they can also be problematic. Genomic instability, and mutations in genes such as those that control the cell cycle and the DNA damage response can increase the risk of developing cancer. For example, germline mutations in ATM, a key protein in HR pathway of DSB repair, leads to Ataxia Telangiectasia (AT), a neurodegenerative disorder. AT sufferers are hypersensitive to DSB-inducing agents such as x-rays, and have a high risk of developing cancer. Deficiencies in NER proteins lead to conditions such as Xeroderma Pigmentosa or Cockayne Syndrome which are characterised by hypersensitivity to UV radiation and an increased risk of skin cancer, and mutations BRCA2, another key HR protein, increase a woman’s risk of developing breast cancer to 60-80% (compared to 13% on average).

Even though deficiencies in DNA repair can predispose to cancer, DNA repair is also emerging as a viable target for cancer therapy. For example, DNA repair inhibitors can be used to sensitise cancer cells to chemotherapy- or radiation-induced damage, making it possible to achieve more tumour cell kill with the same dose of radiation or chemotherapy. However, this approach is not yet used clinically and a major complication is that it often increases both the efficacy as well as the toxicity of treatment.

Another approach is the idea of “synthetic lethality”, which relies on a cancer cell being dependent on a specific DNA repair pathway because it is defective in another, such that deficiency of either one of two pathways is sustainable, but loss of both leads to cell death. This concept was first described by Calvin Bridges in 1922 in a study of fruit flies and is now used in the treatment of breast cancer in the form of an inhibitor of Poly-ADP ribose polymerase (PARP), a key enzyme in the repair of SSBs. Loss of PARP function leads to increased DSBs after cell division due to unrepaired SSBs, which in normal tissue are removed by the DSB repair system. However, BRCA2-deficient tumours are defective in HR and cannot repair the very toxic DSBs, leading to cell death. Therefore, BRCA2-deficient tumours are hypersensitive to PARP inhibitors, which are now an approved therapy for advanced BRCA2-deficient breast and ovarian cancer.

PARP inhibitors are a good example of a so-called “target therapy” for cancer, which is the concept of targeting the molecular characteristics that distinguish the tumour cell from healthy cells (in this case, BRCA2 deficiency), as opposed to most older, cytotoxic chemotherapies, which generally target rapidly dividing cells by inducing DNA damage, and can actually lead to second cancers. With an improved understanding of the molecular differences between normal and tumour cells, cancer therapy is slowly moving away from non-specific cytotoxic drugs towards more tolerable and effective treatments.

From String to Strand

 

By Jordana Lovett

 

Ask a molecular biologist what image DNA conjures up in the mind. A convoluted ladder of nitrogenous bases, twisting and coiling dynamically. Pose the very same question to a theoretical physicist- chances are that DNA takes on a completely different meaning. As it turns out, DNA is in the eye of the beholder. Science is about perspective. Moreover, it relies on the convergence of distinct, yet interrelated angles to tackle scientific questions wholly.

 

When I met Dr. Vijay Kumar at a Cancer Immunotherapy meeting, I was immediately intrigued by his unique background and path to biology.  Vijay largely credits his family for strongly instilling in him core values of education and assiduousness. He was raised to strive for the best, and was driven to satisfy the goals of his parents, who encouraged him to pursue a degree in electrical engineering. While slightly resentful at the time, he now realizes that this broad degree would afford him multiple career options as well as the opportunity to branch into other fields of physics in the future. As early as his teenage years, Vijay had already begun thinking about the interesting unknowns of the natural universe. With his blinders on, he sought to explore them using physics and math, both theoretically and practically. As he advanced to university in pursuance of a degree in electrical engineering, he strategized and planned what would be his future transition into theoretical physics. He dabbled in various summer research projects and sought mentorship to help guide his career. Vijay ultimately applied and was accepted to a PhD program at MIT, where he studied string theory in a 6-dimensional model universe. He describes string theory as a broad framework rather than a theory that can be related to the world through ‘thought experiments’ and mathematical consistency.  Kumar continued his work in string theory during a post-doc in Santa Barbara, California, where he found himself surrounded by a more diverse group of physicists. Theoretical physicists, astrophysicists, and biophysicists were able to intermingle and share their science.

 

This diversity spurred new perspectives and reconsideration of what he had originally thought would be a clear road to professorship and a career in academia. As one would imagine, the broader impacts of string theory are limited; the ideas are part of a specialized pool of knowledge available to an elite handful. Even among the few, competition was fierce- at the time, there were only two available openings for professors in string theory in the United States. Additionally, seeing the need and presence of ‘quantitative people’ in other fields, such as biology made him increasingly curious about alternatives to the automated choices he had been making until this point. With the support of his (now) wife, and inspiration from his brother (who had just completed a degree in statistics/informatics and started a PhD in biology), he networked with other post-docs and set up meetings with principle investigators (PI’s) to discuss how he, as a theoretical physicist, could play a role in a biological setting. He spent time during his post-doc in Santa Barbara, and throughout his second post-doc at Stony Brook reflecting, taking courses and shifting into a different mindset. Vijay interviewed and gave talks at a number of institutions, and eventually landed in lab at Cold Spring Harbor, where he now is involved in addressing some of the shortcomings in DNA sequencing technology.

 

Starting in a different lab within the confines of a field means readjusting to brand new settings, acquainting with new lab mates and shifting from one narrowly focused project to another. Launching not only into a new lab, but into a foreign field adds an extra unsettling and daunting layer to the scenario.  Vijay, however, viewed this as yet another opportunity to uncover mysteries in nature- through a new perspective.  He recognized an interplay between string theory, wherein the vibration of strings allows you to make predictions about the universe, and biology, where the raw sequence of DNA can inform the makeup of an organism, and its interactions with the world.  It is with this viewpoint that Vijay understands DNA. He sees it as an abstraction, as a sequence of letters that allows you to draw inferences and predict biological outcomes. A change or deletion in just one letter can have enormous, tangible effects. It is this tangibility that speaks to Vijay. He is drawn to the application and broader consequences of the work he is doing, and excited that he can use his expertise to contribute to this knowledge.

 

While approaching a radically different field can impose obstacles, Kumar sees common challenges in both physics and biology and simply avoids getting lost in scientific translation. Just as theory has a language, so too biology has its own jargon. Once past this barrier, addressing gaps in knowledge becomes part of the common scientific core. Biology enables a question to be answered through various assays and allows observable results to guide future experiments- expertise in various subjects is therefore not only encouraged, but necessary. Collaborations between different labs across various disciplines enable painting a complete picture. “I’m a small piece of a larger puzzle, and that’s ok”, says Vijay. His insight into how scientists ought to work is admirable. Sharing and communicating data in a way that is comprehendible across the scientific playing field will more quickly and efficiently allow for scientific progress.

 

If I’ve learned one thing from Vijay’s story, it is to understand that science has room for multiple perspectives. In fact, it demands questions to be addressed in an interdisciplinary fashion. You might question yourself along the way. You might shift gears, change directions. But these unique paths mold the mind to perceive, ask, challenge, and contribute in a manner that no one else can.

How to Be Unhappy in Grad School

By Deirdre Sackett

 

If you follow The Oatmeal, you may have seen his newest comic, “How to be perfectly unhappy.” (If you don’t know The Oatmeal, I suggest you check him out! Looking past the crude humor and poop jokes, cartoonist Matthew Inman produces some pretty inspiring, touching, and hilarious comics.) The comic is based off of an essay by Augusten Burroughs, titled “How to Live Unhappily Ever After.”

 

When I saw that title, and even before I read the comic, I immediately thought of the graduate school experience. Not just my own, per se, but the general concept of graduate school — the image of the over-worked, over-caffeinated student plugging away at their fifth 14-hour day that week, with an equally exhausting work-filled weekend to look forward to. Are we, as graduate students, happy with this life? Well, it’s a bit more complicated than that.

 

From a young age, we are programmed to believe that happiness is the ultimate goal in life. Once you obtain it, then you’re golden, and you’ll never have to suffer ever again. You’ve reached Happiness™. But if you’re not happy, then you must be unhappy. And if you’re unhappy, well, then you’re doing something horribly wrong, and you must hate your life. Right? Here’s my bold claim. Despite their busy lives, regardless of the sardonic jokes and grumblings, most graduate students are not Unhappy™. They are not doing anything objectively wrong, nor do they utterly hate their lives. As a grad student, when someone asks, “Are you happy in your grad program?”, it limits an entire 5 to 6 year experience to one word. This innocent question creates a binary in what should be a spectrum of human emotion. It binds the grad student to one of two answers: yes and no.

 

Yes, my experiments all were successful. I have 5 first-author publications, all accepted on the first round with perfect reviews. I’m graduating in 4 years rather than 5 or 6, and I’m guaranteed a starting salary of $100K in my new job. I don’t even have to take a post doc!

 

No, everything is failing. I can’t get statistical significance on anything. My one measly paper got desk rejected by 3 journals. My experiments all yield null results. I can’t network to save my life, and I have no friends. Even my cat hates me.

 

Of course, those are both ridiculous examples. Graduate school is a mixture of good and bad experiences. In the 5 or 6 years it takes to get a Ph.D., you might get one first author publication, a couple of desk rejections, one experiment that works sort-of perfectly and another two that completely fail. You might have two really close friends and a smattering of acquaintances you interact with only at the department holiday party each winter. It’s a blend of good and bad, which makes sense. You don’t waltz into graduate school expecting everything to go perfectly.

 

Like the grad school experience, human emotion doesn’t work in terms of purely Happy or purely Unhappy. Nor should we expect to waltz into our experience and come out happy. The spectrum of emotion ebbs and flows like waves in the ocean, much like progress in graduate school.

 

I’m a graduate student in the sciences, and science is hard work. Experiments don’t go the way I plan, things take longer than I think, and my inexperience slows me down as I learn new techniques. My eyes sting as I stare at a computer screen for 8+ hours a day, analyzing data or writing a paper. I feel guilt and soul-crushing defeat when I can’t write as well or as fast as I expect myself to. Imposter syndrome rumbles in the depths of my brain like a voracious beast, ready to snap up any imperfections I throw its way.

 

And yet, to shamelessly quote The Oatmeal’s comic, what I do is meaningful to me. Everything I do in grad school pushes me to become a better scientist, communicator, and writer. I recognize my frustration at how slowly I analyze data or figure out a technique, and realize that it’s better to slowly do things correctly rather than rush and do it wrong. Each experimental failure encourages me to think creatively and problem-solve, to figure out what went wrong and how I can fix it in the future. Plus, when experiments do succeed, the past failures makes the victory way more significant. Getting negative reviews on a paper help make my science writing better —  they do not reflect on my imperfections as a scientist. Most importantly to me, I know fighting the imposter syndrome beast helps me find self-worth and value in my being, though it’s the hardest thing to do.

 

So it’s not a matter of finding “happiness” in a slew of “unhappy” experiences. It’s a matter of finding value in frustrating or sad experiences and emerging as a different person. Not a happier person, but a stronger person.  Other grad students might feel this exact same way, or at least some version of it. Grad students are in their programs because they find their work meaningful, not because every day is a walk in the park. Other people will question this version of “happy,” and even try to dissuade grad students from doing what they are passionate about because they perceive this existence as blatantly “unhappy.” How to be unhappy is not for others to decide, but for you, dear grad student. So go forth, find meaning in your failures, rejoice in your successes, and thrive in unhappiness.