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

Tracing the ancestry and migration of HIV/AIDS in America

by Arpita Myles

Acquired immunodeficiency syndrome or AIDS is a global health problem that has terrified and intrigued scientists and laypeople alike for decades. AIDS is caused by the Human Immunodeficiency Virus, or HIV, which is transmitted through blood, semen, vaginal fluid, and from an infected mother to her child ^[1]. Infection leads to failure of the immune system, increasing susceptibility to secondary infections and cancer, which are mostly fatal. Considerable efforts are being put into developing prophylactic and therapeutic approaches to tackle HIV-AIDS, but there is also interest in understanding how the disease became so wide-spread. With the advent of the Ebola and Zika viruses in the last couple of years, there is a renewed urgency in understanding the emergence and spread of viruses in the past in order to prevent those in the future. The narrative surrounding the spread of HIV has been somewhat convoluted, but a new paper in Nature by Worobey et. al, hopes to set the record straight ^[2].

Humans are supposed to have acquired HIV from African chimpanzees- presumably as a result of hunters coming in contact with infected blood, containing a variant of the virus that had adapted to infect humans. The earliest known case of HIV in humans was detected in 1959 in Kinshasa, Democratic Republic of the Congo, but the specific mode of transmission was never ascertained ^[3].

There has been little or no information about how HIV spread to United States, until now. HIV incidences were first reported in the US in 1981, leading to the recognition of AIDS ^[4]. Since the virus can persist for a decade or more prior to manifestation of symptoms, it is possible that it arrived in the region long before 1981. However, since most samples from AIDS patients were collected after this date, efforts to establish a timeline for HIV’s entry into the states met with little success. Now, researchers have attempted to trace the spread of HIV by comparing genetic sequences of contemporary HIV strains with blood samples from HIV patients dating back to the late 1970’s ^[2]. These samples were initially collected for a study pertaining to Hepatitis B, but some were found to be HIV seropositive. This is the first comprehensive genetic study of the HIV virus in samples collected prior to 1981.

The technical accomplishment of this work is significant as well. In order to circumvent the problems of low amounts and extensive degradation of the viral RNA from the patient samples, they developed a technique they call “RNA jackhammering.”  In essence, a patient’s genome is broken down into small bits and overlapping sequences of viral RNA are amplified. This enables them to “piece together” the viral genome, which they can then subject to phylogenetic analysis.

Using novel statistical analysis methods, Worobey et al. reveal that the virus had probably entered New York from Africa (Haiti) during the 1970s, whereupon it spread to San Francisco and other regions. Upon analyzing the older samples, the researchers found that despite bearing similarities with the Caribbean strain, the strains from San Francisco and New York samples differed amongst themselves. This suggests that the virus had entered the US multiple, discreet times and then began circulating and mutating. Questions still remain regarding the route of transmission of the virus from Haiti to New York.

The relevance of this study is manifold. Based on the data, one can attempt to understand how pathogens spread from one population to another and how viruses mutate and evolve to escape natural immunity and engineered therapeutics. Their molecular and analytical techniques can be applied to other diseases and provide valuable information for clinicians and epidemiologists alike. Perhaps the most startling revelation of this study is that contemporary HIV strains are more closely related to their ancestors than to each other. This implies that information derived from ancestral strains could lead to development of successful vaccine strategies.

Beyond the clinic and research labs, there are societal lessons to be learned as well. Published in 1984, a study by CDC (Center for Disease Control) researcher William Darrow and colleagues traced the initial spread of HIV in the US to Gaétan Dugas- a French Canadian air steward. Examination of Dugas’s case provided evidence linking HIV transmission with sexual activity. Researchers labeled Dugas as “Patient O”, as in “Out of California” ^[5]. This was misinterpreted as “Patient Zero” by the media- a term still used in the context of other epidemics like flu and Ebola. The dark side of this story is that Dugas was demonized in the public domain as the one who brought HIV to the US. As our understanding of the disease and its spread broadened, scientists and historians began to discredit the notion that Dugas played a significant role. However, scientific facts were buried beneath layers of sensationalism and hearsay and the stigma remained.

Now, with the new information brought to light by Worobey’s group, Dugas’s name has been cleared. Phylogenetic analysis of Dugas’s strain of HIV was sufficiently different from the ancestral ones, negating the possibility that he initiated the epidemic.

The saga in its entirety highlights the moral dilemma of epidemiological studies and the extent to which the findings should be made public. Biological systems are complicated, and while narrowing down origin of a disease has significance clinical relevance, we often fail to consider collateral damage. The tale of tracking the spread of HIV is a cautionary one; scientific and social efforts should be focused more on resolution and management, rather than on vilifying unsuspecting individuals for “causing” an outbreak.

References:

1. Maartens G, Celum C, Lewin SR. HIV infection: epidemiology, pathogenesis, treatment, and prevention. Lancet. 2014 Jul 19;384(9939):258-71.

2. Worobey M, Watts TD, McKay RA et al., 1970s and 'Patient 0' HIV-1 genomes illuminate early HIV/AIDS history in North America. Nature. 2016 Oct 26. doi: 10.1038/nature19827.

3. Faria NR, Rambaut A et al., HIV epidemiology. The early spread and epidemic ignition of HIV-1 in human populations. Science. 2014 Oct 3;346(6205):56-61.

4. Centers for Disease Control (CDC). Pneumocystis pneumonia--Los Angeles. MMWR Morb Mortal Wkly Rep. 1981 Jun 5;30(21):250-2.

5. McKay RA. “Patient Zero”: The Absence of a Patient’s View of the Early North American AIDS Epidemic. Bull Hist Med. 2014 Spring: 161-194.

NIH to chimera researchers: Let's talk about this...

by Chris Yarosh

When we think about the role of the National Institutes of Health (NIH) in biomedical research, we often think only in terms of dollars and cents. The NIH is a funding agency, after all, and most researchers submit grants with this relationship in mind. However, because the NIH holds the power of the purse, it also plays a large role in dictating the scope of biomedical research conducted in the U.S. It is noteworthy, then, that the NIH recently delayed some high profile grant applications related to one type of research: chimeras.

Chimeras, named for a Greek mythological monster composed of several different animals, are organisms that feature cells that are genetically distinct.  In the lab, this commonly refers to animals that contain cells from more than once species. Research into chimeras is not new; scientists have been successfully using animal/animal (e.g. sheep/goat) chimeras for over 30 years to learn about how animals develop. Human/animal chimeras are also a common research tool. For example, the transfer of cancerous human tissue into mice with weakened immune systems is standard practice in cancer biology research because it allows researchers to test chemotherapy drugs in a system that is more complex than a dish of cells before testing them in human subjects. These experiments are largely uncontroversial, save for individuals who fall into the anti-animal testing camp (and those who dispute the predictive power of mouse models in general). Why then, has the NIH decided to pump the brakes on this line of research?

Like many things, the answer lies in the timing. The temporarily-stalled research involves injecting human pluripotent cells—undifferentiated cells that can develop into any number of different cell types—not into mature animals, but instead into animal embryos. Unlike the tumor-in-a-mouse research mentioned above, this kind of experiment is specifically trying to get normal human cells to develop as an animal matures and remain, well, normal human cells. One idea is that someday we could grow an organ (liver, pancreas, etc.) in an animal, such as a pig, that is still a human organ. This would lower the barrier for successful transplantation, meaning that somebody in serious need of a new liver could receive one from livestock instead of waiting for a human donor from a transplant list. Another thought is that chimeric animals will better model human physiology, making subsequent clinical trials more accurate.

If you read the last paragraph and felt a bit uneasy, you’re not alone. For some, this type of research crosses the invisible line that separates humans from animals, and is therefore unacceptable. Others find this research troubling from an animal welfare standpoint, and still other worry about unanticipated differentiation (e.g. “we wanted a liver, but we found some human cells in the pig’s nerves, too”) or unethical uses for this type of technology.

The NIH hears these concerns, and wants to talk about them before giving scientists the go ahead to use public funds on this type of research. Some researchers have reacted negatively to this, fearing broader restrictions in the future, but I think this is an important part of the scientific process. We live (and for scientists, work) in an era of unprecedented ability to modify genomes and cell lineages, and human/animal chimeras are just one example of a type of research destined for more attention and oversight. It is important to get the guidelines right.

The NIH will convene a panel of scientists and bioethicists to discuss human/animal chimera research on November 6^th, so keep an eye out for possible policy revisions after then. Given the promise of this type of research and the potential concerns over its use, this surely is only the beginning of the deliberative process.

UPDATE (11/05/2015): Scientists from Stanford University have posted an open letter in Science calling for a repeal of the current restrictions in this field. The full letter, found here, argues that there is little scientific justification for the NIH's stated concerns. Over at Gizmodo,  the NIH has responded by claiming that the true purpose of the stop order and review is to "stay ahead" of current research and anticipate future work. This is consistent with the NIH's views as articulated on the Under the Poliscope blog. All things considered, the workshop tomorrow, and any guidelines resulting from it, should be very interesting for people who wish to develop and use these tools.

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.

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