UPenn Scientists Are Investigating Better Treatments for Sarcoma Tumors

by Adrian Rivera-Reyes and Koreana Pak

Soft tissue sarcomas (STS) are rare cancers of the connective tissues, such as bone, muscle, fat, and blood vessels. Soft and elastic, sarcoma tumors can push against their surroundings as they grow silent and undetected. Residing in an arm, torso, or thigh, it can take years before a sarcoma begins to cause pain. By the time a patient presents their tumor to a doctor, amputation may be unavoidable¹.

In 2017, it is predicted that 12,390 Americans will be diagnosed with sarcoma, and approximately 5,000 patients will die from these tumors². But the vast majority of these patients aren’t dying from the first tumor in their arm or leg—the real danger is metastasis, which is responsible for more than 90% of cancer-related deaths^3-5.

Metastasis occurs when tumor cells leave their original site and colonize a new area of the body, such as the lungs, liver, or bones^3-5. The current treatment options for sarcoma—surgery, chemotherapy, and radiation—are not very effective against metastases^6,7. Only 10-25% of STS patients respond to chemotherapy, leaving surgery as the best option for many^6,7. However, tumor cells can spread to other parts of the body even in early stages of sarcoma, long before the first tumor is even noticed. By the time the tumor is surgically removed, metastases have usually developed in other parts of the body.

As a sarcoma tumor grows, it becomes increasingly starved of oxygen and nutrients. Under these conditions, cancer cells are driven to metastasize. Moreover, tumor hypoxia, or low oxygen levels, are an important predictor of metastasis and low survival in sarcoma patients^8-10. In other words, the more tumor hypoxia, the lower a patient’s chance of surviving.

But how does this actually work? How does hypoxia drive sarcoma cells out of a tumor and into other organs, such as the lungs? Surprisingly, UPenn scientists have found it has a lot to do with collagen¹¹!

Metastasizing tumor cells (pink) associated with collagen (blue). Image taken by Koreana Pak.

Collagen is the most abundant protein in the human body, but you’ll know it best as the substance that makes your skin flexible and elastic¹². This elastic material has many uses, and you can find it in gelatin, marshmallows, surgical grafts—and hypoxic tumors. In STS tumors, the low oxygen levels cause collagen to form sticky, tangled fibers.  Sarcoma cells will actually hijack this disorganized collagen and use it as a “highway” over which they can migrate out of the tumor and into other organs¹¹.

If these hypoxic collagen “highways” were disrupted in patient tumors, cancer cells could be prevented from metastasizing. But how?

In an effort to make this therapy a reality, UPenn scientists used models of human sarcoma and metastasis in which they could disrupt collagen. By deleting the hypoxia factors HIF-1 and PLOD2, they could restore normal collagen in tumors, which reduced tumor metastasis. Excitingly, they also found that minoxidil, a drug usually used to treat hair-loss, also reduced tumor collagen and halted metastasis¹¹.

Whether minoxidil could be used for human patients is unclear; nevertheless, drugs that reduce hypoxic targets like PLOD2 could serve as promising anti-metastatic therapies.

In a follow up study, these scientists looked at another hypoxic factor, called HIF-2¹³. While related to HIF-1, this protein actually plays a very different role in sarcoma. Elimination of HIF1 is important because it reduces metastasis¹¹. But when it comes to primary sarcoma tumors, the expression of HIF-2 can help reduce cancer cell growth¹³.

Again using a model of human sarcoma, the authors found they could increase tumor size when they eliminated HIF-2. They also used a clinically approved drug, Vorinostat, to treat these tumors, and saw that HIF-2 increased and as a consequence the tumors to shrank¹³.

Sarcoma Treatment: Going Forward

The diversity of STS, which comprises about 50 different types¹, as well as the low incidence of cases, makes it very challenging to develop better treatments for sarcoma. Clinical trials often combine patients with different types of sarcomas into a single study, even though the trial may not be a good fit for all the patients. A more specific approach is needed to treat the different types of sarcomas.

Through their research on hypoxia in sarcoma, UPenn scientists hope to improve current treatments. Their observation that HIF-1 and HIF-2 play opposing roles in different cancers is of particular importance, because HIF inhibitors are already being developed for cancer therapy^11,13. Doctors can also use markers like HIF-2 to predict how well patients will respond to different treatments. For example, patients with tumors that have low levels of HIF-2 will respond well to treatments with Vorinostat. Unfortunately, such predictive markers are rare in STS, and the identification of additional markers should complement the development of new treatments.

Complementing standard chemotherapy with new sarcoma-specific therapies would greatly improve current treatment options. However, treating the primary tumor alone is not sufficient, as metastasis remains primarily responsible for patient death^6,7. For this reason, further study into HIF-1/PLOD2 and the role of collagen in metastasis is needed. Through the development of drugs like minoxidil, which target harmful tumor collagen, we see exciting potential for the future of sarcoma therapy and patient survival.

References

1. Cancer.Net Editorial Board. (2012, June 25). Sarcoma, Soft Tissue – Introduction. Retrieved on April 4, 2017 from: http://www.cancer.net/cancer-types/sarcoma-soft-tissue/introduction

2. The American Cancer Society medical and editorial content team. (2017, January 6). What Are the Key Statistics About Soft Tissue Sarcomas? Retrieved on April 4, 2017 from https://www.cancer.org/cancer/soft-tissue-sarcoma/about/key-statistics.html

3. Mehlen, P., & Puisieux, A. (2006). Metastasis: a question of life or death. Nature Reviews Cancer, 6, 449-458.

4. Monteiro, J. & Fodde, R. (2010). Cancer stemness and metastasis: therapeutic consequences and perspectives. European Journal of Cancer, 46 (7), 1198-1203.

5. Nguyen, D.X., Bos, P.D., & Massagué, J. (2009). Metastasis: from dissemination to organ-specific colonization. Nature Reviews Cancer, 9, 274-284.

6. Linch, M., Miah, A. B., Thway, K., Judson, I. R., & Benson, C. (2014). Systemic treatment of soft-tissue sarcoma-gold standard and novel therapies. Nat. Rev. Clin. Oncol. 11(4), 187-202.

7. Lorigan, P., Verweij, J., Papai, Z., Rodenhuis, S., Le Cesne, A., Leahy, M.G., Radford, J.A., Van Glabbeke, M.M., Kirkpatrick, A., Hogendoom, P.C., & Blay, J.Y. (2007). Phase III trial of two investigational schedules of ifosfamide compared with standard-dose doxorubicin in advanced or metastaic soft tissue sarcoma: a European Organization for Research and Treatment of Cancer Soft Tissue and Bone Sarcoma Group Study. Journal of Clinical Oncology 25 (21), 3144-3150.

8. Shintani, K., Matsumine, A., Kusuzaki, K., Matsubara, T., Santonaka, H., Wakabayashi, T., Hoki, Y., & Uchida, A. (2006). Expression of hypoxia-inducible factor (HIF)-1 alpha as a biomarker of outcome in soft-tissue sarcoma. Virchows Arch. 449 (6), 673-681. 

9. Nordsmark, M., Alsner, J., Keller, J., Nielsen, O.S., Jensen, O.M., Horsman, M.R., & Overgaard, J. (2001). Hypoxia in human soft tissue sarcomas: adverse impact on survival and no association with p53 mutations. Br. J. Cancer 84 (8), 1070-1075. 

10. Rajendran, J.G., Wilson, D.C., Conrad, E.U., Peterson, L.M., Bruckner, J.D., Rasey, J.S., Chin, L.K., Hofstrand, P.D., Grierson, J.R., Eary, J.F., & Krohn, K.A. (2003). [(18)F]FMISO and [(18)F]FDG PET imaging in soft tissue sarcomas: correlation of hypoxia, metabolism, and VEGF expression. Eur. J. Nucl. Med. Mol. Imaging, 30 (5), 695-704.

11. Eisinger-Mathason, T.S.K., Zhang, M., Qiu, Q., Skuli, N., Nakazawa, M..S., Karakasheva, T., Mucaj, V., Shay, J.E., Stangenberg, L., Sadri, N., Puré, E., Yoon, S.S., Kirsch, D.G., & Simon, M.C. (2013). Hypoxia dependent modification of collagen networks promotes sarcoma metastasis. Cancer Discovery, 3 (10), 1190-1205.

12. What is collagen? Retrieved on April 4, 2017 from http://www.vitalproteins.com/what-is-collagen.

13. Nakazawa, M.S., Eisinger-Mathason, T.S., Sadri, N., Ochocki, J.D., Gade, T.P., Amin, R.K., & Simon, M.C. (2016). Epigenetic re-expression of HIF-2 alpha suppresses soft tissue sarcoma growth. Nature Communications, 7, 10539

Event Recap: Intellectual Property Panel “From Research to Patent”

by Adrian Rivera-Reyes

On November 10^th, the Penn Science Policy Group and the Penn Intellectual Property Group at Penn Law co-hosted a panel discussion focused on intellectual property and how to patent scientific research. The panel included Peter Cicala, Chief Patent Counsel at Celgene Corp.; Dr. Dora Mitchell, Director of the UPstart Program at the Penn Center for Innovation (PCI) Ventures; and Dr. Michael C. Milone, Assistant Professor of Pathology and Laboratory Medicine at the Hospital of the University of Pennsylvania (HUP), and Assistant Professor of Cell and Molecular Biology at Penn Medicine.

The event started with the introduction of both groups by their respective presidents and was proceeded by Kimberly Li giving an introduction of the panelists. Next, Peter gave a short PowerPoint presentation with a general introduction of intellectual property. Below are some key points to understand intellectual property/patent law ^1,2:

1) In general, patents provide a “limited monopoly” that excludes others from making an invention, using, offering for sale, selling, or otherwise practicing an invention, but it does not confer upon the patentee a right to use the said invention. Thus, patents serve as a form of protection for the owner.

2) A single invention can only be patented once; once the patent on that invention expires, others may not file to patent the same invention again.

3) In order to confer a patent, the United States Patent and Trademark Office ensures that inventions of patentable subject matter meet the following legal requirements: i) inventions must be novel, ii) inventions must be useful, and iii) inventions must be non-obvious.

4) Utility patents only last for 20 years from the date of filing. After 20 years, anyone can make, use, offer for sale, sell, or practice the invention. A single invention cannot be re-patented after the time is done. In contrast, trademarks or trade secrets last forever, and copyrights last for the lifetime of the author.  

5) The United States Patent and Trademark Office follows the ‘first to file’ rule. Thus, the first person or entity to file a patent is the assumed owner.

6) Patents can be invalidated by the United States Patent and Trademark Office.

A clever example discussed by Peter Cicala was the patenting of a new car feature. If X company has submitted and received a patent for a car and Y company makes a new feature for the car, they can patent the new feature (as long as it meets the legal requirements introduced above). Once the patent for the new feature is conferred to Y company then they can produce that one feature, but not the car that was patented by X company, unless a license is provided by X company to Y company. Thus, the patent for Y company only gives them the power to prevent others from making that new feature.

Conferring Patents in the US and Internationally

First, there has to be an invention of some sort. Once there is an invention, a patent is filed. Patents are drafted free-hand, unlike a tax application where one has a specific form to fill. For patents, one has to start from scratch. Patents are usually long (some can reach 500 pages in length) and there are many legal requirements on what to say in the application and how to say it. Eventually, when one files a patent application it will go to the patent office. A patent examiner will, as the name suggests, examine it and deliberate with the patent office over the course of 3-5 years as they point out sections that need further editing, clarification, or justification. There is a lot of back and forth, until the examiner agrees that the invention has satisfied the patent requirements. Then, one pays fees and the patent is awarded. Fun fact: In the US, patents are granted only on Tuesdays.

On a global basis, one files a single international patent and the designated patent offices around the world examine it locally. If an office grants a patent, such patent will only be valid in that jurisdiction. That is why submitting patents cost so much, because one files and pays legal fees for each jurisdiction. For example, if a patent is filed in Japan for a compound, a different entity can manufacture the compound freely in the US, but not in Japan. This is one reason why companies and universities are very careful when filing patents.

Intellectual Property in Industry

Pharmaceutical products start with a great idea, but for every product in the market there are about 10,000 that fail. Therefore, companies file many patents even though many of those patents may not have any commercial value in 5-6 years. It costs about $500K to file (including filing and attorneys’ fees) and receive a single issued patent, which means companies spend a lot in patents (i.e. 10,000 patent submissions each worth $500K)! Out of those 10,000 patents, typically one will make the company about an estimated $5 billion a year in returns.

A student asked, “Is submitting a patent the same price for a university as it is for a company?” In essence, no! The patent office makes a distinction between large and small entities. Small entities, based on requirements provided by the patent office³, pay half the fees, but attorneys charge a fixed price. In the end, small entities save just a small percentage of money. Another question asked by an audience member was “what is patentable in the pharma business?” If one patents a molecule, no one else can infringe or use that molecule itself. That is how companies patent drugs or their associated components. One can also patent dosing regimens, formulations, modes of administration, etc. The compound claim gives the most protection, because it is very hard to make a knock-off of a molecule.

Intellectual Property in Academia

A student raised the issue that there is a lot of communication that occurs in science, especially at conferences, symposia, or amongst colleagues, classmates, etc. That seems to be a big risk in the context of protecting one's intellectual property, but doing so is an unavoidable risk when one does scientific research.

Dora, patent analyst from PCI Ventures, then proceeded to discuss the issues brought up from an academic perspective. She said, “The question raised here is that when one works in an academic institution the work is knowledge based and disseminated to others.... How does one draw the line from all that to protect something valuable?” What most, if not all, academic/research institution do is have their lawyers work very closely with faculty, so that anytime they are about to publish a paper, go to a conference, attend grand rounds, or any other such public appearance, the lawyers will hustle and get an application submitted before such events.

In addition to these more public forums, problems can arise from talking with friends who are not directly associated with the work. An example of this pertains to OPDIVO®, a drug patented by Ono Pharmaceuticals and the Kyoto University in the 90’s, which later was exclusively licensed to Bristol-Myers Squibb who launched the drug. Recently, Dana Farber Cancer Institute sued Ono Pharmaceuticals and Bristol-Myers Squibb because the principal investigator at Kyoto University had periodically consulted a colleague at Dana Farber for his advice. The professor-consultant at Dana Farber would send some data he thought was helpful and consult with them. Dana Farber sued both companies, claiming that the now-retired professor from its institution should be included as an inventor in the patent. Because an inventor of a patent is part-owner, Dana Farber is actually claiming ownership of the patent and will receive compensation from the sales of products under the patent^4,5.

Michael, Penn Med professor who works intimately with a team of lawyers from PCI because he regularly files patents, said that balancing confidentiality with science communication is a difficult task. He commented, “I think it comes down to how important one thinks the invention is and a lot of the times the patent will not get developed if it will not bring any money to the owner (company/institution).” Moreover, there has to be a conversation with the university because the university pays for the patent, so it decides what to file. It also depends on the resources of the university. Regarding the work of graduate students or postdoctoral fellows, there are more considerations. Students and postdocs want and need to publish, go to conferences, and present their work in order to move forward with their careers; thus patents can be a rather limiting step for them.

From the industry perspective, Peter clarified that the rule at Celgene is that no one can talk about anything until the patent application is filed. Once the patent application is filed, employees are free to talk to whomever they wish without causing a situation like the one with Dana Farber and Bristol-Myers Squibb, since the patent application has been filed prior to any communication.

Thus, a clear difference between industry and academia is that in industry, things are kept under wraps and then a patent is filed, whereas in academia patents are filed early to make sure that the institution does not lose the rights of patenting by making the information public. Because universities file very early, there is a lot to deal with afterwards. The costs of prosecution are high, and sometimes the application does not make it through the full process, because universities cannot afford to throw $500K for an application if they are not confident on getting a return on the investment. The reason to file for some universities might be purely strategic.

Ownership vs. Inventorship

Another interesting topic discussed, was that of ownership vs. inventorship. There is the notion that ownership follows inventorship. In most cases, people do not file patents on their own; they work for companies or universities. Usually, an employment contract will state that if an employee invents something while employed by that entity, then ownership to a resultant patent will be assigned to the employer. Thus, the person is the inventor but not the owner of the patent; the entity is the owner. For academic research, the Bayh-Dole act was enacted to allow universities to own inventions that came from investigations funded by the federal government⁶. Dora explained that, “Government officials got together and agreed that they awarded so much money into research and good stuff came out of it, which the government would own but not file patents or do anything with it commercially."

A preliminary list of inventors is written when the patent is filed, but legally the inventors are the people that can point to a claim and say: "I thought of that one." Inventors have to swear under oath that they thought of a particular claim, and need to be able to present their notebooks with the data supporting a claim of inventorship. Inventors are undivided part-owners of the patent, which means that any inventor listed in the patent can license that patent in any way, without accounting for any of the other inventors. Additionally, there is a difference between the people that think about the claims and the people that actually execute the subject matter of the resulting claim. If a person is only executing experiments without contributing intellectually to the idea or procedure, then that person is not an inventor. For those in academic research, this often differs from how paper authorship is decided – usually performing an experiment is sufficient.

Summary

The discussion prompted the researchers in the room to be on the lookout for ideas they have that can result in patents, and to be careful when discussing data and results with people outside of their own research laboratory. Also, the discussion exposed key differences between intellectual property lawyers working for universities and industries, as opposed to law firms that have departments working on intellectual property. Ultimately, students felt they gained a basic understanding on how intellectual property works, the rules to file patents, and some intrinsic differences between academic and industry research.

References:

1) United States Patent and Trademark Office – (n.d.) Retrieved December 11, 2016 from https://www.uspto.gov/patents-getting-started/general-information-concerning-patents

2) BITLAW – (n.d.) Retrieved December 11, 2016 from http://www.bitlaw.com/patent/requirements.html

3) United States Patent and Trademark Office – (n.d.) Retrieved December 20, 2016 from https://www.uspto.gov/web/offices/pac/mpep/s2550.html

4) Bloomberg BNA – (2015, October 2) Retrieved December 11, 2016 FROM https://www.bna.com/dana-farber-says-n57982059025/

5) United States District Court (District Court of Massachusetts). http://www.dana-farber.org/uploadedFiles/Library/newsroom/news-releases/2015/dana-farber-inventorship-complaint.pdf

6) National Institute of Health, Office of Extramural Research – (2013, July 1) Retrieved December 11, 2016 from https://grants.nih.gov/grants/bayh-dole.htm

WHO says bacon causes cancer?

by Neha Pancholi

Note: Here at the PSPG blog, we like to feature writing from anyone in the Penn community interested in the science policy process or science for general interest. This is the 1st in a series of posts from new authors. Interested is writing for the blog? Contact us!

The daily meat consumption in the United States exceeds that of almost every other country¹. While the majority of meat consumed in the United States is red meat², the consumption of certain red meats has decreased over the past few decades due to associated health concerns, such as heart disease and diabetes^1,2. In October, the World Health Organization (WHO) highlighted another potential health concern for red meat: cancer.

The announcement concerned both red and processed meat. Red meat is defined as unprocessed muscle meat from mammals, such as beef and pork³. Processed meat– generally red meat –has been altered to improve flavor through processes such as curing or smoking³. Examples of processed meat include bacon and sausage. The WHO confirmed that processed meat causes cancer and that red meat probably causes cancer. Given the prevalence of meat in the American diet, it was not surprising that the announcement dominated headlines and social media. So how exactly did the WHO decide that processed meat causes cancer?

The announcement by the WHO followed a report from the International Agency for Research on Cancer (IARC), which is responsible for identifying and assessing suspected causes of cancer. The IARC evaluates the typical level of exposure to a suspected agent, results from existing studies, and the mechanism by which the agent could cause cancer.

After a review of existing literature, the IARC classifies the strength of scientific evidence linking the suspected cancer-causing agent to cancer. Importantly, the IARC determines only whether there is sufficient evidence that something can cause cancer. The IARC does not evaluate risk, meaning that it does not evaluate how carcinogenic something is. The IARC classifies the suspected carcinogen into one of the following categories⁴:

• Group 1 – There is convincing evidence linking the agent to cancer in humans. The agent is deemed carcinogenic.
• Group 2A – There is sufficient evidence of cancer in animal models, and there is a positive association observed in humans. However, the evidence in humans does not exclude the possibility of bias, chance, or confounding variables. The agent is deemed as a probable carcinogen.
• Group 2B – There is a positive association in humans, but the possibility of bias, chance, or confounding variables cannot be excluded. There is inadequate evidence in animal models.
• This category is also used when there is sufficient evidence of cancer in animal models, but there is not an association observed in humans. The agent is a possible carcinogen.
• Group 3 – There is inadequate evidence in humans and animals. The agent cannot be classified as carcinogenic or not carcinogenic.
• Group 4 – There is sufficient evidence to conclude that the agent is not carcinogenic in humans or in animals.

The IARC reviewed over 800 studies that examined the correlation between consumption of processed or red meat and cancer occurrence in humans. These types of studies, which examine patterns of disease in different populations, are called epidemiological studies. The studies included observations from all over the world and included diverse ethnicities and diets. The greatest weight was given to studies that followed the same group of people over time and had an appropriate control group. Most of the available data examined the association between meat consumption and colorectal cancer, but some studies also assessed the effect on stomach, pancreatic, and prostate cancer. The majority of studies showed a higher occurrence of colorectal cancer in people whose diets included high consumption of red or processed meat compared to those who have low consumption. By comparing results from several studies, the IARC determined that for every 100 grams of red meat consumed per day, there is a 17% increase in cancer occurrence. For every 50 grams of processed meat eaten per day, there is an 18% increase. The average red meat consumption for those who eat it is 50-100 grams per day.³

The IARC also reviewed studies that examined how meat could cause cancer. They found strong evidence that consumption of red or processed meat leads to the formation of known carcinogens called N-nitroso compounds in the colon. It is also known that cooked meat contains two types of compounds that are known to damage DNA, which can lead to cancer. However, there is not a direct link between eating meat containing these compounds and DNA damage in the body.³

Based on the strong evidence demonstrating a positive association with consumption of processed meat and colorectal cancer, the IARC classified processed meat as a Group 1 agent³. This means that there is sufficient evidence that consumption of processed meat causes cancer.

There was a positive association between consumption of red meat and colorectal cancer in several epidemiological studies. However, the possibility of chance or bias could not be excluded from these studies. Furthermore, the best-designed epidemiological studies did not show any association between red meat consumption and cancer. Despite the limited epidemiological evidence, there was strong mechanistic evidence demonstrating that red meat consumption results in the production of known carcinogens in the colon. Therefore, red meat was classified as a probable carcinogen (Group 2A)³.

It will be interesting to see how the WHO announcement affects red meat consumption in the United States and worldwide. But before swearing off processed and red meat forever, there are a few things to consider.

First, it is important to bear in mind that agents classified within the same group have varying carcinogenic potential. Processed meat was classified as a Group 1 agent, which is the same classification for tobacco smoke. However, estimates by the Global Burden of Disease Project attribute approximately 34,000 cancer deaths per year to consumption of processed meat⁵. In contrast, one million cancer deaths per year are due to tobacco smoke⁵. While the evidence linking processed meat to cancer is strong, the risk of cancer due to processed meat consumption appears to be much lower than other known carcinogens. Second, the IARC did not evaluate studies that compared vegetarian or poultry diets to red meat consumption⁵. Therefore, it is unknown whether vegetarian or poultry diets are associated with fewer cases of cancer. Finally, red meat is high in protein, iron, zinc, and vitamin B12³. Thus, while high red meat consumption is associated with some diseases, there are also several health benefits of consuming red meat in moderation. Ultimately, it will be important to balance the risks and benefits of processed and red meat consumption.

¹http://www.npr.org/sections/thesalt/2012/06/27/155527365/visualizing-a-nation-of-meat-eaters

²http://www.usda.gov/factbook/chapter2.pdf

³Bouvard et al. Carcinogenicity of consumption of red and processed meat. The Lancet Oncology, 2015. 16(16): 1599-1600.

⁴http://www.iarc.fr/en/media-centre/iarcnews/pdf/Monographs-Q&A.pdf

⁵http://www.who.int/features/qa/cancer-red-meat/en/

Penn Science Spotlight: Learning how T cells manage the custom RNA business

Chris Yarosh

This Science Spotlight focuses on the research I do here at Penn, the results of which are now in press at Nucleic Acids Research¹. You can read the actual manuscript right now, if you would like, because NAR is “open access,” meaning all articles published there are available to anyone for free. We’ve talked about open access on this blog before, if you’re curious about how that works. 

First, a note about this type of science. The experiments done for this paper fall into the category of “basic research,” which means they were not designed to achieve an immediate practical end. That type of work is known as “applied” research. Basic research, on the other hand, is curiosity-driven science that aims to increase our understanding of something. That something could be cells, supernovas, factors influencing subjective well-being in adolescence, or anything else, really. This isn’t to say that basic research doesn’t lead to advances that impact people’s lives; quite the opposite is true. In fact, no applied work is possible without foundational basic work being done first. Rather, the real difference between the two categories is timeline and focus: applied research looks to achieve a defined practical goal (such as creating a new Ebola vaccine) as soon as possible, while basic research seeks to add to human knowledge over time. If you’re an American, your tax dollars support basic research (thanks!), often through grants from the National Institutes of Health (NIH) or the National Science Foundation (NSF). This work, for example, was funded in part by two grants from the NIH: one to my PhD mentor, Dr. Kristen Lynch (R01 GM067719), and the second to me (F31 AG047022). More info on science funding can be found here.

Now that you've gotten your basic research primer, let's talk science. This paper is primarily focused on how T cells (immune system cells) control a process called alternative splicing to make custom-ordered proteins. While most people have heard of DNA, the molecule that contains your genes, not everyone is as familiar with the RNA or proteins. I like to think of it this way: DNA is similar to the master blueprint for a building, specifying all of the necessary components needed for construction. This blueprint ultimately codes for proteins, the molecules in a cell that actually perform life’s work. RNA, which is “transcribed” from DNA and “translated” into protein, is a version of the master blueprint that can be edited as needed for different situations. Certain parts of RNA can be mixed and matched to generate custom orders of the same protein, just as you might change a building’s design based on location, regulations, etc. This mixing and matching process is called alternative splicing (AS), and though it sounds somewhat science-fictiony, AS naturally occurs across the range of human cell types.

While we know AS happens, scientists haven’t yet unraveled the different strategies cells use to control it. Part of the reason for this is the sheer number of proteins involved in AS (hundreds), and part of it is a lack of understanding of the nuts and bolts of the proteins that do the managing. This paper focuses on the nuts and bolts stuff. Previous work2 done in our lab has shown that a protein known as PSF manipulates AS to produce an alternate version of a different protein, CD45, critical for T cell response to antigens (bits of bacteria or viruses). PSF doesn’t do this, however, when a third protein, TRAP150, binds it, although we previously didn’t know why. This prompted us to ask two major questions: How do PSF and TRAP150 link up with one another, and how does TRAP150 change PSF’s function?

My research, as detailed in this NAR paper, answers these questions using the tools of biochemistry and molecular biology. In short, we found that TRAP150 actually prevents PSF from doing its job by binding in the same place RNA does. This makes intuitive sense: PSF can’t influence splicing of targets it can’t actually make contact with, and it can't contact them if TRAP150 is gumming up the works. To make this conclusion, we diced PSF and TRAP150 up into smaller pieces to see which parts fit together, and we also looked for which part of PSF binds RNA. These experiments helped us pinpoint all of the action in one region of PSF known as the RNA recognition motifs (RRMs), specifically RRM2. Finally, we wanted to know if PSF and TRAP150 regulate other RNA molecules in T cells, so we did a screen (the specific technique is called “RASL-Seq,” but that’s not critical to understanding the outcome) and found almost 40 other RNA molecules that appear to be controlled by this duo. In summary, we now know how TRAP150 acts to change PSF’s activity, and we have shown this interaction to be critical for regulating a bunch of RNAs in T cells.

So what are the implications of this research? For one, we now know that PSF and TRAP150 regulate the splicing of a range of RNAs in T cells, something noteworthy for researchers interested in AS or how T cells work. Second, we describe a mechanism for regulating proteins that might be applicable to some of those other hundreds of proteins responsible for regulating AS, too. Finally, PSF does a lot more than just mange AS in the cell. It actually seems to have a role in almost every step of the DNA-RNA-protein pathway. By isolating the part of PSF targeted by TRAP150, we can hypothesize about what PSF might do when TRAP150 binds it based on what other sections of the protein remain “uncovered.” It will take more experiments to figure it all out, but our data provide good clues for researchers who want to know more about all the things PSF does.

A map of the PSF protein. Figure adapted from Yarosh et al., WIREs RNA 2015, 6: 351-367. doi: 10.1002/wrna.1280

Papers cited:

1.) Christopher A. Yarosh; Iulia Tapescu; Matthew G. Thompson; Jinsong Qiu; Michael J. Mallory; Xiang-Dong Fu; Kristen W. Lynch. TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells. Nucleic Acids Research 2015;

doi: 10.1093/nar/gkv816

2.) Heyd F, Lynch KW. Phosphorylation-dependent regulation of PSF by GSK3 controls CD45 alternative splicing. Mol Cell 2010,40:126–137.

Penn researchers interview HIV-positive adolescents in Botswana to better understand the factors affecting adherence to antiretroviral treatments

Of the more than three million children infected with HIV, 90% live in Africa. As HIV-positive children become adolescents, it is important that antiretroviral treatments are maintained to protect their own health, as well as to safeguard the adolescents from developing resistant strains of HIV and to prevent infection of other individuals.

HIV-positive adolescents’ adherence to these treatments has been identified as a public health challenge for Botswana. However, the assessment tools testing psychosocial factors that are likely associated with poor adherence have been developed in Western countries and their constructs may not be relevant to African contexts. A new study published in PLOS ONE by Penn researchers Elizabeth Lowenthal and Karen Glanz described the cultural adaptation of these assessment tools for Botswana.

The psychosocial assessments investigate factors that may affect adolescents’ adherence to antiretroviral treatments. As Lowenthal summarized, “one of the key reasons why adolescents with HIV have higher rates of death compared with people with HIV in other age groups is that they have trouble taking their medications regularly.”

Researchers looked at the following factors by testing 7 separate assessment scales developed with Western cohorts for their applicability to Botswanan adolescents.

• Psychological reactance- an aversion to abide by regulations that impose upon freedom and autonomy
• Perceived stigma
• Outcome expectancy- whether treatments were expected to improve health
• Consideration of future consequences- the extent to which adolescents plan for their futures rather than focusing on immediate gains
• Socio-emotional support- how adolescents receive the social and emotional support they need

The researchers interviewed 34 HIV-positive Botswanan adolescents in depth, sub grouped by age in order to talk about the factors in ways participants could understand.

The study confirmed the construct validity of some assessment tools, but highlighted four areas that caused tools to not relate to participants:

• Socio-emotional support for the adolescents mostly came from parents rather than peers.
• Denial of being HIV infected was more common than expected.
• Participants were surprisingly ambivalent about taking their medicine.

Some of the tools (psychological reactance, future consequences) required major modifications to obtain construct validity for adolescents with HVI in Botswana.The assessment tools were modified during the course of the study based on participant feedback. Future research will test the association between these modified assessment tools and HIV treatment outcomes in order to provide insight into how to best support HIV infected adolescents.

First author Lowenthal suggested that the study could inform studies of adolescent adherence to other treatments as well, stating that “questions that we are able to answer in our large cohort of HIV-positive adolescents will likely be generalizable to other groups of adolescents with chronic diseases.”

-Barbara McNutt 

Penn researchers identify novel therapeutic target for kidney cancer

Kidney cancer, also known as renal cancer, is one of the ten most common cancers in both men and women. The American Cancer Society’s most recent estimates state that of the predicted 63,920 new cases of kidney cancer this year, roughly 20% of  patients will die from the disease. By far, the most common type of kidney cancer is renal cell carcinoma (RCC). The majority of RCCs are clear cell RCCs (ccRCCs), a subtype characterized by metabolic alterations, specifically increased carbohydrate and fat storage. More than 90% of ccRCCs have been found to have mutations in the von Hippel-Lindau (VHL) tumor suppressor gene; however, kidney specific VHL deletion in mice does not induce tumorigenesis or cause metabolic changes similar to those seen in ccRCC tumors. So what additional factors are needed for ccRCC tumor formation and progression? A recent study by Penn researchers published in the journal Nature identified the rate-limiting gluconeogenesis enzyme fructose-1,6-bisphosphatase (FBP1) as a key regulator of ccRCC progression.

To better understand ccRCC progression, the study’s first author, Bo Li, a post-doctoral researcher in the lab of Dr. Celeste Simon, performed metabolic profiling on human ccRCC tumors while also analyzing ccRCC metabolic gene expression profiles. Compared to the adjacent normal kidney tissue, ccRCC tumors had increased amounts of metabolites involved in sugar metabolism and significantly lower expression of carbohydrate storage genes, including FBP1. Further investigation revealed FBP1 expression was reduced in almost all tumor samples tested (>600) and reduced FBP1 expression strongly correlated with advanced tumor stage and poor patient survival. Thus, understanding the role of FBP1 in ccRCCs could significantly impact the treatment of this disease.

How do reduced levels of FBP1 promote ccRCC tumor progression? The authors found that FBP1 depletion in ccRCC cells stimulates growth and relieves inhibition of sugar breakdown (glycolysis), which provides energy for the growing cancer cells. In addition, VHL mutations associated with ccRCCs prevent the degradation of a transcription factor that responds to decreases in oxygen, known as hypoxia-inducible factor α (HIFα), thus stabilizing it. Stabilized HIFα does not cause FBP1 depletion, but its activity is tightly regulated by FBP1. This study emphasized the importance of the interaction between HIFα and FBP1, particularly when glucose and oxygen levels are low, for the formation and progression of the ccRCC.

Why is this work so important? Little is known about how changes in cell metabolism contribute to the formation and progression of ccRCC tumors. As stated by Li, “elucidating how FBP1 impacts the altered metabolic and genetic programs of ccRCC improves our knowledge of the molecular details accompanying ccRCC progression, and identifies novel therapeutic targets for this common malignancy.” Future work may focus on identifying how FBP1 is suppressed and whether reversing FBP1 suppression could improve patient outcomes. 

-Renske Erion

Purdue professor Dr. Sanders responds to commentary about his Ebola interview with Fox News

Last month I analyzed the media coverage of Ebola in a post where I dissected an interview between Fox News reporters and Dr. David Sanders. I was recently contacted by Dr. Sanders, who wished to clarify a few issues that I raised in my article. The purpose of my post was to demonstrate how the media sometimes covers scientific issues in ways that exaggerate and oversimplify concepts, which can potentially mislead non-scientist citizens.

I stated that the way Dr. Sanders described his research sounded a little misleading. I intended to convey how I thought an average non-scientist listener might interpret the dialogue. However, Dr. Sanders points out that he was careful with his wording to avoid possible confusion. He explained, “as you have pointed out, one says one thing, and the media (and the Internet) render it as something else.  I would just like to point out that I carefully stated that Ebola can ENTER human lung from the airway side; I never said infect.  I also try to avoid the use of the term ‘airborne’ because of the confusion about its meaning.”

Also, he had several good scientific points about the validity of using pseudotyped viruses and the comparison to other viruses when considering the potential for a change in Ebola transmission.

“Pseudotyped viruses are used widely for studying viral entry, and I know of no examples where the conclusions on the cell biology of the entry of pseudotyped viruses have been contradicted by studies of entry of the intact virus despite such comparisons having been published numerous times.” 

“When we discovered that there was maternal-child transmission of HIV was that a new mode of transmission or merely a discovery of a previously unknown mode of transmission? How was Hepatitis C transmitted between humans before injections and blood transfusions? I don't know either. How is Ebola virus transmitted between fruit bats or from fruit bats to humans? Perhaps modes of transmission differ in their efficiency. The HIV comparison with Ebola ("HIV hasn't become airborne") is fallacious given the cell biology of entry for the two viruses.  The receptors for HIV (the CD4 attachment factor and the chemokine receptor) are present on blood cells and not on lung tissue.  The receptors for Ebola are present on a diverse set of cells including lung cells. In addition, Influenza A switches in real time from a gastrointestinal virus in birds to a respiratory virus in mammals--not that many mutations required.”

Additionally, he wisely pointed out that “precedent may be a valid argument in medical practice or the law, but it is not valid in science.” In fact, science seeks to uncover things that were previously unknown, and thus were without precedent.

I appreciate Dr. Sander’s response to my article. I think that rational and in-depth discussions about science need to happen more frequently in the media. Short, simplified stories with shock-factor headlines only detract from the important conversations that are necessary to find practical solutions to challenges like Ebola.

-Mike Allegrezza

Penn researchers identify neurons that link circadian rhythms with behavioral outcomes.

Our bodies evolved to alternate rhythmically through sleep and wake periods with the 24-hr cycle of the day. These “circadian rhythms” are controlled by specific neurons in the brain that act as molecular clocks. The experience of jet lag when we change time zones is the out-of-sync period before the brain’s internal clock re-aligns with the external environment.

How does this molecular clock work in the brain? Decades of research have uncovered that environmental signals, such as light, are integrated into a circadian clock by specific neurons in the brain. However, little is understood about how these circadian clock cells drive biological effects such as sleep, locomotion, and metabolism. A study by Penn researchers published earlier this year in Cell has discovered critical neural circuits linking the circadian clock neurons to behavioral outputs.

The researchers used the fruit fly Drosophila as a model organism because like humans, they also have circadian rhythms, yet they are very easy to manipulate genetically and many powerful tools exist to study the 150 circadian clock neurons in their brains. The study found that a crucial part of the circadian output network exists in the pars intercerebralis (PI), the functional equivalent of the human hypothalamus.

“Flies are normally active during the day and quiescent at night, but when I activate or ablate subsets of PI neurons, they distribute their activity randomly across the day,” describes the study’s first author, Daniel Cavanaugh, PhD, a post-doc working in the lab of Amita Sehgal, PhD. Importantly, the research showed that modulating the PI neurons lead to behavioral changes without affecting the molecular oscillations in central circadian clock neurons, indicating that the PI neurons link signals from the circadian clock neurons to behavioral outputs.

The study also showed that the PI neurons are anatomically connected to core clock neurons using a technique involving the fluorescent protein GFP. Cavanaugh explains, “The GFP molecule is split into two components, which are expressed in two different neuronal [cell] populations. If those populations come into close synaptic contact with one another, the split GFP components are able to reach across the synaptic space to reconstitute a fluorescent GFP molecule, which can be visualized with fluorescence microscopy.”

Additionally, their experiments showed that a peptide called DH44, a homolog to the mammalian corticotropin-releasing hormone, is expressed in PI neurons and important for maintaining circadian-driven behavioral rhythms.

While these new data are interesting for understanding general mechanisms of biology, they also have implications for human health and disease.

“People exposed to chronic circadian misalignment, such as occurs during shift work, show increased rates of heart disease, diabetes, obesity, cancer, and gastrointestinal disorders,” says Cavanaugh. “In order to understand the connection between circadian disruption and these diseases, we have to understand how the circadian system works to control the physiological outputs that underlie these disease processes.”

-Mike Allegrezza

Fox News demonstrates both good and bad ways to cover Ebola

Some news outlets, including Fox, have been wildly spreading fears about Ebola. As an example of both good and bad ways that the media covers science, let’s take a look at a recent clip from Fox News in which they interview Dr. David Sanders about the possibility of Ebola virus mutating to become airborne-transmissible (right now it is only spread by direct contact!)

Their story is titled "Purdue professor says Ebola 'primed' to go airborne." Here is a link to the video.

I’ll start off with the good things:

1) Dr. Sanders did a good job explaining that Ebola is not airborne right now, but there is a "non-zero" probability that Ebola might mutate to infect the lungs and become air transmissible. And this probability increases as more people are infected.

2) The newscasters did a good job of accurately recapping what he was explaining without blowing it out of proportion.

Now for some bad things:

1) Quite obviously, the scare-you-into-clicking-on-it title. First of all, it's completely misleading for the sole purpose of grabbing attention (it got me!). Second of all, it's completely false. I watched it three times and Dr. Sanders never said "primed." So it is blatantly incorrect.

2) They did not include coverage of other scientists that claim the fears of airborne transmission are over-hyped because there are no instances of that ever happening naturally for a virus that infects humans. HIV and hepatitis are both good examples that have infected millions without changing their route of transmission.

3) The way Dr. Sanders describes his published research is a little misleading in the context of this story. It sounds like he describes the research demonstrated Ebola virus can infect the lungs. In fact, the actual study showed that if you take some of the proteins from the surface of Ebola and code them into a completely different virus (in this case a feline lentivirus, similar to HIV), you can infect human airway epithelial cells grown in cell culture. So this research did not use the full Ebola virus, and did not demonstrate this infection in a live animal model. Link to study here: http://www.ncbi.nlm.nih.gov/pubmed/12719583

Some of these negative aspects might be a consequence of the brevity of this story. However, in an information-dense world, people get the news in short snippets, so the media needs to be careful not to compromise accuracy.

Interestingly, on the same network, Shep Smith reported on Ebola with commendable accuracy. He communicated the facts clearly and concisely while criticizing “hysterical” reporting as “irresponsible.” 

I hope future reports from Fox News and the rest of the media follow his tone.

*Update Nov 19, 2014: A follow up to this post detailing a thoughtful response from Dr. Sanders can be found here.

-Mike Allegrezza

Welcome!

Welcome to the Penn Science Policy Group.  We are a group of scientists interested in the relationship between science and public policy, examining how both domains affect each other to shape our society.  

Our mission is:

1) To educate scientists about the process of science policy, namely how research and public policy can inform and guide each other.

2) To advocate for research and improve communication of science to the public.

3) To provide resources and training for scientists interested in developing a career in science policy.


We achieve these goals by discussing current issues in interactive monthly meetings, receiving career information from speakers and info sessions, and refining relevant skills through written and oral public communication.  

Whether you are planning a science policy career, or simply looking to stay abreast with important issues, we are here to help you learn about and navigate the field of science policy. 

For more information, please email penn.science.policy@gmail.com.

Thanks,
PSPG