Recent publications from the PS-OC network

Human breast cancer cells. (Image created by Shyam Khatau/ Wirtz Lab)

Human breast cancer cells. (Image created by Shyam Khatau/ Wirtz Lab)

Johns Hopkins Physical Sciences-Oncology Center is part of a network of centers studying how physical forces affect the spread of cancer. Every quarter, the National Cancer Institute complies a list of recent publications from all the participating centers. So if you want to keep up with what the Johns Hopkins PS-OC and other groups have been up to on their quest to discover the physical science mechanisms behind metastasis, look no further than this list which you can download here.

Using the physicals sciences to study cancer offers a new approach over the “traditional” genetic means of studying the disease. To learn more about the unique philosophy behind the NCI’s PS-OC network of centers visit this link.

Nanotechnology for gene therapy

Editor’s Note: The following is a summary of one of the talks from the 2013 Nano-bio Symposium hosted by Johns Hopkins Institute for NanoBioTechnology held May 17. This summary was written by Randall Meyer, a doctoral candidate in the biomedical engineering and a member of the Cancer Nanotechnology Training Center. Look for other symposium summaries on the INBT blog.

One of the key features of nanotechnology is its wide range of applicability across multiple biological scenarios ranging from gene therapy to immune system modulation. Jordan Green, an assistant professor of Biomedical Engineering at Johns Hopkins University, summarized some of the fascinating applications of nanotechnology on which his laboratory has been working. Green is an INBT affiliated faculty member.

One of the Green lab projects involves the design and implementation of nanoparticle based vectors for delivery of genetic material to the cell. Green demonstrated how these particles could be used to deliver DNA and induce expression of a desired gene, or small interfering RNA (siRNA) to silence the expression of a target gene. These genetic therapeutics are being developed to target a wide variety of retinal diseases and cancers.

Jordan Green (Photo by Marty Katz)

Jordan Green (Photo by Marty Katz)


As opposed to viral based vectors for gene therapy, nonviral vectors such as nanoparticles are safer, more flexible in their range of cellular targets, and can carry larger cargoes than viruses, Green explained.


Another project in the Green lab involves the development of micro and nano dimensional artificial antigen presenting cells (aAPCs) for cancer immunotherapy. These aAPCs mimic the natural signals that killer T-cells receive when there is an invader (bacteria, virus, cancer cell, etc.) in the body. The Green lab is currently working with these particles to stimulate the immune system to fight melanoma.


Green Group

Taking a digital perspective on cancer

Editor’s Note: This story was written by Bryan Kohrs, a junior in Biophysics at Johns Hopkins University  with a strong interest in science writing and science. It first appeared in the 2013 issue of Nano-Bio Magazine.

Denis Wirtz lines up next to many other scientists in the war on cancer. But while others battle with familiar technologies and ideas, Wirtz has armed himself with a new imaging technology, a fresh strategy on how to better combat this dreaded disease and a five year grant from the National Cancer Institute (NCI).

Wirtz, a professor of Chemical and Biomolecular Engineering at Johns Hopkins, is carving out a niche for himself in cancer research by focusing on the look and physical structure of cancerous cells rather than the genes from which the cells originated. He believes that this technology will not only help doctors predict how cancer progresses, but will eventually change the way cancer is treated from a therapeutic standpoint. The technology is the keystone of the new Johns Hopkins Center for Digital Pathology, which Wirtz directs.

To understand how this technology works, consider this analogy: A cell is like a Lego brick. Just as individual Legos can come together to create a building, millions of different cells come together to make a human being. Certain bricks serve different purposes in a building in the same way that distinctive cells carry out certain functions in the body. The properties that make some Legos better suited for one purpose over another are their size and shape. For example, if a piece is flat and wide, it should go on the base. Structural characteristics that make cells unique include overall size, shape, the size and shape of the different cell parts or organelles, the composition of certain organelles, and hundreds of other parameters.

Pei-Hsun Wu of the Wirtz lab examining pancreatic cancer cells. (Photo by Mary Spiro)

Pei-Hsun Wu of the Wirtz lab examining pancreatic cancer cells. (Photo by Mary Spiro)

Wirtz’s technology uses a modified scanning electron microscope and a process called high-throughput cell phenotyping (HTCP) to instantly make hundreds of thousands of highly specific measurements defining each of these structural cellular characteristics of each single cell on a slide. Wirtz has software that uses an algorithm that adds up all of the different measurements and gives a cell a structural “score,” which quantifies the look of the cell with a number. The process will be automated and will take just minutes for a slide of cells to be analyzed and given an overall structural score, which averages the scores of all the cells on the slide.

Anirban Maitra, a professor of Oncology and Pathology at Johns Hopkins School of Medicine who is collaborating with Wirtz on this project, explains the benefits of automating this process, “If you were looking at a cell with the naked eye, you would say it has a large nucleus, medium sized nucleus, or a small nucleus. What automation allows you to do is to spread that crude three-tiered category into hundreds of small denominational events that you could then objectively add up and get a score.”

Over the course of the next five years, Wirtz plans to use HTCPanalysis as a clinically applicable tool that can help doctors treat cancer patients with more personalized therapies.

“Currently, we have a very crude approach to therapy even with the targeted therapies that are being developed. The vast majority of patients in cancer care and oncology get what are called cytotoxic agents, the old agents that were made many years ago,” said Maitra. But by using HTCP to see how cancers that look a certain way respond to certain treatments, doctors will be able to better personalize cancer treatments.

To make the project clinically applicable, Wirtz, with the help of Maitra and Ralph Hruban, also a professor of Oncology and Pathology at Johns Hopkins School of Medicine who is collaborating with the team, will be working to create the first “phenotypic database,” or a cell-feature-focused database. It will combine patient data like age, sex, cancer type, progression, treatment used, genetic sequencing results (analysis of tumor from a genetic standpoint), and so forth in an online, “cloud” database and then also add in the structure score of the patient’s tumor performed from HTCP.

At the moment, Hopkins is the only university with Wirtz’s new technology. The plan is for hospitals across the nation to begin uploading patient information to the database online and sending slides of cancer tumor cells to Hopkins or an alternate research facility using this technology. There, independent researchers will analyze the cells and add the HTCP analysis to the patient information online.

Denis Wirtz, right, working with recent PhD graduate Shyam Khatau. (Photo Will Kirk/Homewood Photography)

Denis Wirtz, right, working with recent PhD graduate Shyam Khatau. (Photo Will Kirk/Homewood Photography)

Doctors can upload all of this data into the cloud and help the database grow initially. Eventually, an oncologist in Chicago,  treating a 70-year-old man with lung cancer, and a HTCP score of X will be able to go online and find that there were two similar patients, a 65-year-old man with lung cancer in Baltimore and a 75-year-old woman with lung cancer in California, both with a score of X as well. The physician would discover that the man in Baltimore was treated with chemotherapy A and died in six months, while the woman in California was treated with chemotherapy B and was cured. Doctors will be able to make more informed treatment decisions.

Classifying the morphological characteristics of cancer is a shift from the traditional genetic approach to categorizing cancer cells. Previously, scientists researched cancer from a genetic standpoint, linking specific genetic mutations to specific cases of cancer. While this has lead to gene-targeted therapies, Wirtz wants to take a different approach to cancer research. He wants to look beyond the genetic origin of cancer and focus on what cancerous cells look like.

“We’ve come to realize that it is the heterogeneity – the diversity of cells that have different characteristics – is also important in evaluating a cancer case. In the end what matters are the cell properties.

That’s what we measure,” Wirtz explained. The rationale for this new approach, Wirtz explained, is that while cells can be identical genetically, they can vary tremendously in structure, just as two identical twins can develop to be very different people, both physically and personally. Cells from one tumor could become metastatic, latch onto a new organ, and start a new tumor that eventually kills the patient, while a genetically identical set of cells could remain localized and die as soon as they detach from the original tumor.

Wirtz’s theory is that the key to cancer treatment prognostication lies not in cancer genetics, but in the physical attributes of cancerous cells. For example, you could say that muscle definition and physical fitness would be strongly correlated with athletics and would therefore be able to be used to predict who out of twenty people would become athletes. Wirtz believes that his technology will allow doctors to do the same thing with cancer.

With this new technology Wirtz hopes to figure out what triggers cancer cells to metastasize. For example, do small, elliptical cells with large nuclei metastasize better than large, rod-like cells with small nuclei? He explained that cells that metastasize have to be super-cells, much like super-heroes are better, faster, and stronger than other humans.

“Millions of cells are shed by tumors every day, but only one or two of them will have what it takes to become metastatic. These  are the decathlon cells. We need to figure out what the physical properties are that give these cells an edge,” Wirtz says.

Maitra poses the question that guides the project in its applications towards therapeutic cancer treatment, “We have a lot of different drugs out there right now. Some work, some don’t. The problem is you only find out if they worked retroactively. You give it to a patient and six months later the metastasis keeps growing and you know if it’s worked or not. But wouldn’t it be nice if we knew going into the treatment that these patients would respond to a particular regimen and these other patients respond to another regimen?”

Maitra believes that conceptually, this project is paradigm shifting. “Wirtz is analyzing cancer in a brand new way. Extending this tool into an open-access cancer database, the project seems to have a bright future for helping doctors treat patients.”

Maitra makes sure to keep the project in perspective while being hopeful about the direction of this project, “It is very preliminary at this point. We have a long way to go before we can actually say this is a clinically applicable technology, but what we are doing right now is working our way up there.”

Center for Digital Pathology

Game Theory and Cancer

What does game theory and cancer have to do with each other. I am not sure but this interesting workshop hosted by the Princeton Physical Sciences-Oncology Center and Johns Hopkins University might help you figure that out.

An announcement about the event reads:

Screen Shot 2013-08-02 at 12.03.06 PMRegistration is now open for the Workshop on Game Theory and Cancer, scheduled on August 12-13 in Baltimore, MD, and jointly hosted by our Princeton PS-OC and Johns Hopkins University. The main goal of this workshop is to provide a dialogue between leading basic researchers and clinical investigators that would help make headway against the very stubborn problem of cancer, and to jolt the oncology community into confronting the serious clinical problems that have previously been avoided.

The flyer is pretty cool, too.  Check it out here.

Additional information and preliminary agenda can be found at:

To register, please go to:

For questions about the event, email or

What’s on the horizon for regenerative medicine?

Organo-electric nanowires.  (Tovar Lab/JHU)

Organo-electric nanowires. (Tovar Lab/JHU)

Editor’s Note: The following is a summary of one of the talks from the 2013 Nano-bio Symposium hosted by Johns Hopkins Institute for NanoBioTechnology held May 17. This summary was written by Christian Pick, a doctoral candidate in the chemical and biomolecular engineering laboratory of Joelle Frechette. Look for other symposium summaries on the INBT blog.

The fundamental goal of regenerative medicine is to allow the body to restore normal function to damaged or diseased tissues. Tissue scaffolds provide a structure for cells to grow on to accomplish this task. The pinnacle of scaffold function would be for the tissue grown from a scaffold to be completely indistinguishable from natural, undamaged tissue.

In order to improve scaffolds, researchers need to better understand how scaffolds interact with the body. Peter Gabriele, Director of Emerging Technology at Secant Medical, discussed FT-IR microscopy,  which is a unique tool that can help researchers with this very task.

Fourier transform infrared (FTIR) spectroscopy is a powerful technique for analyzing the chemical identity of materials. FTIR spectroscopy has been used for years in forensic analysis for identifying unknown samples. FTIR microscopy combines the functionality of FTIR spectroscopy with optical microscopy.

For the field of regenerative medicine, this means that the surface functionality of a scaffold can be mapped and studied throughout its entire lifetime: from production through degradation in-vivo. For instance, FTIR microscopy can be used to analyze surface modifications made to a scaffold during fabrication.

Additionally, it can be used to track tissue formation in implanted scaffolds. As an example, Mr. Gabriele described studies on “biorubber” or poly(glycerol sebacate) (PGS). FTIR microscopy has been used to identify collagen integration within the polymer during implantation as well as map the erosion of the material once implanted. Through the use of tools such as FT-IR microscopy, researchers can continue to expand the functionality of tissue scaffolds.

Secant Medical

Watch a video about INBT’s current research efforts in the realm of regenerative medicine here.

Beauty is in the eye of the microscopist

Scientists have been using microscopes to produce up-close views and gather data about cells and other tiny things for more than 400 years. Many times, however, those images are not just informative, they are beautiful.


Actin network in mouse fibroblast (Image by Dong-Hwee Kim)

Dong-Hwee Kim, a postdoctoral fellow in the Institute for NanoBioTechnology in the Whiting School of Engineering, frequently uses microscopy in his research on cell mechanics, a field he describes as “one of the fastest growing interdisciplinary fields in biology.”

Several of his images have not only yielded abundant quantitative and qualitative data, but they have netted him awards for scientific imaging.

In 2011 he earned an Image of Distinction Award from the Nikon Small World Competition for his photo of a dis-organized perinuclear actin cap stress fibers in a mouse embryonic fibroblast. That same year, he was awarded an Honorable mention from the American Society for Cell Biology 7th Annual Cell Biology film contest for his movie “Hurricane: Cell Cytoplasm Movements”. And in 2013, Kim took second place in the Biophysical Society’s, The Art of Science Image Contest for his dandelion-like representation of the geodesic actin network in a mouse fibroblast.

Kim says his primary focus in collecting these images has always been purely for scientific purposes. “I am trying to better understand how cells recognize the physical properties of the cell environment and respond to them,” he said.

Engineers have developed theories about cell mechanics and about what they expect to happen at the single cell level. But instead of describing the cell’s response with a computational model or other simulation, Kim was determined to capture actual images of live cells reacting to their surroundings.

Perinuclear actin cap stress fibers in a mouse embryonic fibroblast (Image by Dong-Hween Kim)

Perinuclear actin cap stress fibers in a mouse embryonic fibroblast (Image by Dong-Hwee Kim)

“Direct visualization of cell functions has become one of the most effective ways to support scientific findings, since it is the simplest but most powerful way to con-vince others,” he said.

Using various microscopy techniques, Kim has been able to visualize cell components, such as the nucleus or actin filaments, in very detailed ways. “It is always exciting to become the first one to show something that others haven’t seen yet,” he said.

Denis Wirtz, Kim’s advisor, noticed how beautiful the postdoc’s images were and suggested that he enter some of his work into popular imaging contests. Each contest focuses on a different theme, but the bottom line is that the images must be scientifically relevant as well as visually interesting. For example, the image of the geodesic actin network in the mouse embryonic fibroblasts, which were used for both the Nikon and Biophysical Society image contests, “directly visualized the mechanical and spatial coordinates of filamentous actin cytoskeleton in the cell,” said Kim. But the images also happen to be reminiscent of dandelions and fireworks.

Even if making a pretty picture is not the intent of the image, Kim thinks that having an artistic eye is important in science.

“I think artistic images in science should be based on a combination of aesthetic discrimination and scientific significance, which gives them unparalleled power to support scientific findings and persuade others,” Kim said.

The old saying goes, “a picture is worth 1,000 words.” In this case an expertly executed scientific image “can overcome myriad arguments,” Kim added.

Kim said his favorite imaging tool is the “confocal laser scanning microscopy, which allows high resolution images in cell biology, as well as qualitative and quantitative analysis of images.” He emphasizes that he does not use any software enhancements, such as Photoshop, to beautify his images. However, by attempting to create a beautiful image, he has developed several new imaging protocols.

“In challenging myself to create artistic images, it has sometimes led me to design new scientific methodologies that were not conventionally used in the field, and I think these efforts can contribute to the advancement of science,” Kim said.

This article was written by Mary Spiro, science writer for INBT at Johns Hopkins University, and first appeared in the 2013 issue of Nano-Bio Magazine.


Advanced Imaging Workshop: BU campus

Advanced Imaging Workshop

August 19-20, 2013,
Imaging Core Facilities, BU campus
9am – 5pm

To register, please reply to this email.

Course Directors:

Phil Allen

Jerome Mertz

Orian Shirihai

This workshop will present an overview of state-of-the-art optical microscopy techniques including phase contrast microscopy, confocal microscopy, two-photon excited fluorescence (TPEF), second-harmonic generation (SHG), structured illumination microscopy (SIM), adaptive optics and light sheet microscopy. The workshop will also include topics specifically tailored to superresolution and nanoscale imaging, as well as some fundamentals, including photo physical properties of fluorescence, sensors, FRET, photo conversion and organelle tracking.

This workshop is open to students and post-docs at Boston University and other Cancer Nanotechnology Training Centers in the NCI Alliance.  Attendance is free of charge, but registration is required.  Registration is on a first come, first served basis and SPACE IS LIMITED!  

To register, please email Brenda Hugot:


High school research internships keep skills fresh

For most teenagers, finding a summer job is almost a rite of passage into adulthood. It’s a chance to learn responsibility and time management and practice how to get along with coworkers. It also helps earn money for college or fun. A group of specially selected teens, however, were able to take the concept of the summer job a step further as summer research scholars in Johns Hopkins University laboratories.

High schooler Christopher Miller with his graduate student mentor Hoku West-Foyle. (Photo by Mary Spiro)

High schooler Christopher Miller with his graduate student mentor Hoku West-Foyle. (Photo by Mary Spiro)

The Summer Academic Research Experience (SARE) program, an opportunity funded in part by Johns Hopkins Institute for NanoBioTechnology and the School of Medicine, trains students from “disadvantaged” homes throughout the state. Some students may have a parent in prison or struggling with addiction. Others may face extreme financial hardship or even have been homeless.

SARE scholars have a chance to overcome obstacles to academic success by working in academia under the guidance of a mentor. They improve their writing and mathematics skills through tutoring. And they learn how to keep good laboratory records, how to follow safety protocols, and how to make a professional presentation.

“This is way better than flipping burgers,” exclaimed Stephanie Keyaka, as she prepared an image of a Western Blot performed on Drosophila eye genes. Keyaka, a tenth grader from The SEED School of Maryland, the state’s only public boarding school. She studied rhodopsin in the eyes of flies in the lab of professor Craig Montell during the summer of 2012.

SARE, launched in 2009 through a collaboration between INBT and School of Medicine cell biology associate professor Doug Robinson, recruits students from the private nonprofit Boys Hope Girls Hope of Baltimore, from The SEED School, and now also from The Crossroads School, operated by the nonprofit Living Classrooms Foundation. While the partnership with Boys Hope Girls Hope has been in place from the beginning, working with The SEED School and The Crossroads School has expanded the potential pool of qualified and interested applicants. “Expanding the applicant pool makes the program more competitive, which is a worthwhile experience—to have to compete for something,” Robinson said.

During their time at Hopkins, each SARE scholar focuses on a mini research project that advances the larger goals of the lab where they are placed. No prior laboratory work is expected, and the learning curve is steep. But with mentoring from graduate students and postdoctoral fellows, the scholars find their way. At the end of the summer, the scholars present their findings in a poster session for their peers, faculty and staff.

“At the beginning of the summer, I didn’t know what the heck I was talking about, but now I get it!” laughed Christopher Miller, a tenth grader from The SEED School. Miller studied the motor protein myosin in the Robinson lab.

Miller’s mentor, cell biology doctoral student Hoku West-Foyle, said working with students during the summer helps to re-energize the lab. “At first, it is a bit of extra work, but it gives you teaching experience, and when you are explaining your project to other people, it helps to reinforce why the larger research question matters. It fires you up to work harder,” West-Foyle said.

Shaolin Holloman, an eleventh grader at Baltimore Polytechnic Institute and Girls Hope scholar, worked in the cell biology lab of professor Carolyn Machamer. Her project sought to understand why the SARS coronavirus localizes to the Golgi apparatus of the cell.

“I liked the work experience because we actually got to do hands-on experiments,” said Hollomon, who hopes to become an orthopedic surgeon. “The biggest challenge for me was to keep up with my weekly essays, my summer reading and the work in the lab.”

Robinson hopes the program can become self-sustaining and even scalable to accept more students. “We are at a juncture where we are seeking additional funding, so we are systematically assessing our impact,” Robinson said. One would judge that the SARE program’s impact is significant, since all five alumni who have graduated from high school, or who will do so this spring, have gone on to university, Robinson reported. Two students have declared biology as their major and the other three still in high school are interested in science, technology, mathematics or health-related disciplines. Five new scholars will join SARE this summer.

Khalek Kirkland, The SEED School headmaster said summer internships of this kind are important to help keep students motivated and on track academically. “We do believe in the ‘summer brain drain,’ in that students do lose something over the summer,” Kirkland explained. “Doug and I are in talks about writing a grant together to expand the program not only to SEED School students, but to additional students as well.”

Anyone with interest in supporting the efforts of the SARE program can contact Douglas Robinson via email a

Story by Mary Spiro

More on the SARE program:

Lab coats are summer gear for high school researchers 

Mesenchymal stem cell-based therapies offer hope

Editor’s Note: The following is a summary of one of the talks from the 2013 Nano-bio Symposium hosted by Johns Hopkins Institute for NanoBioTechnology held May 17. This summary was written by Randall Meyer, a doctoral candidate in the biomedical engineering and a member of the Cancer Nanotechnology Training Center. Look for other symposium summaries on the INBT blog.

Among many of the therapies developed over the past several years, stem cells remain one of the most promising for purposes of regeneration, autoimmune disease, and cancer treatment.

Gabriele Todd of Osiris Therapeutics.

Gabriele Todd of Osiris Therapeutics.

Gabrielle Todd, a senior scientist at Osiris Therapeutics, explained some the new mesenchymal stem cell (MSC) based therapies that the company has been developing over the past several years during her talk at the annual Nano-Bio Symposium, hosted by Johns Hopkins Institute for NanoBioTechnology.

The key features that make MSCs such an attractive option is their ability to be isolated from a patient, expanded ex vivo, and re-infused into the same or possibly a different patient. Once inside the body they will home to the site of trouble and release anti-inflammatory and regenerative signals to the damaged tissue. In addition, these cells are what is known as “immune privileged,” in that they lack the necessary signals to trigger an immune response, customary in other transfusions.

Todd summarized some applications on which the company is currently working. One is an MSC-based therapy that utilizes the unique properties of these cells to treat a wide variety of immune related diseases such as graft vs. host disease, Crohn’s disease, and tissue damage from cardiac arrest to juvenile diabetes.

A second application is a product that utilizes MSCs immobilized in a membrane and applied to the site of an external wound. This cells then mediate regeneration of the external tissues, allowing for more efficient healing.

Todd reports that some of these therapies could be available on the market in the coming years.

Osiris Therapeutics, Inc. 

Nano-bio film students in crunch mode for film fest

Every summer I teach Communication for Scientists and Engineers (EN 670.609) to the students in the Johns Hopkins Institute for NanoBioTechnology graduate training programs. The course is a crash course in how to present science to non-technical audiences in an engaging way, that is, as film. We have just a few class sessions and then several weeks of out of class for filming and editing.

Each time I teach the course I change it a little. The first year, it was all writing. The next year I switched to video, and the students made videos about their own research. We did that for a couple more years. This year, however, I changed it again, and two teams are working on videos with slightly broader scope. One film will explain what nanotechnology is and the other will discuss regenerative medicine.

Team 1 working on "what is nanobiotechnology.

Team 1 working on “what is nanobiotechnology?”.

Today, the teams are in crunch mode to get their films done. They will probably be a little longer than the ones classes have made in the past, but hopefully they will be packed with interesting content. I invite you to come see what they have created at the INBT Film Festival on Wednesday, July 24 at 10:45 a.m. in 101 Remsen Hall on the Homewood campus. No RSVP is required. This event is open to the entire Hopkins community, including visitors.

During the premiere, the students will discuss some of the challenges they had in constructing their film and share what they learned during the process. I don’t expect the students to come out as filmmakers, although some have had the opportunity to make research-related videos later on in their graduate student careers. What I do hope, is that they understand how challenging it can be to explain a complex topic to people who don’t know much about science or engineering.

After the premiere, the videos will be uploaded to the INBT YouTube page, which you can find here.

This year’s students included:

Team 2 working on "what is regenerative medicine."

Team 2 working on “what is regenerative medicine?”.

Team 1 – John-michael Williford, Gregory Wiedman, Gregg Duncan and Nuala Del Piccolo

Team 2 – Herdeline Ardoña, Jason Lee, Jennifer Poitras and Charles Hu.