Faculty Research 2018
Cell-free DNA may be key to monitoring urinary tract infections
A new method for testing urinary tract infections yields more information than what conventional methods can offer, according to new research from investigators at Weill Cornell Medicine, Cornell’s Meinig School of Biomedical Engineering and NewYork-Presbyterian.
In a study published June 20 in Nature Communications, researchers analyzed pieces of DNA, called cell-free DNA, isolated from the urine of kidney transplant patients. They discovered that this DNA provides valuable information about the bacterial and viral composition found within patients’ urine.
“With just one test, many pieces of information about bacteria and viruses, as well as antibiotic resistance, can be determined at the same time,” said co-lead author Iwijn De Vlaminck, assistant professor of biomedical engineering.
De Vlaminck said he hopes to do a validation study to see if this test can be implemented into practice. This new test not only could be important for kidney transplant patients, who frequently contract viral and bacterial urinary tract infections, but also for the general population.
“Urinary cell-free DNA is a versatile analyte for monitoring infections of the urinary tract.” Philip Burnham, Darshana Dadhania, Michael Heyang, Fanny Chen, Lars F. Westblade, Manikkam Suthanthiran, John Richard Lee & Iwijn De Vlaminck. Nature Communications 9, Article number: 2412 (2018).
New microscopy method could benefit study of migrating cancer cells
Assistant professor Steve Adie and team have come up with a way to use pressure from pulses of laser light to create sub-nanometer shifts of micrometer-sized particles embedded in soft tissue-like media. The displacement of the particles is measured by a second beam in a process called photonic-force optical coherence elastography (PF-OCE).
The first beam “jiggles the beads up and down,” Adie said, and their displacement values are measured using optical coherence tomography—a second laser beam—giving the researchers an idea of the local mechanical properties of the medium surrounding each bead.
This technique, recently published in Nature Communications, has the potential to change how biomedical scientists study the relationship between cells and their environment, particularly when using engineered tissue cultures such as organoids. It also allows for time-lapse 3D mechanical microscopy, something that was not possible using traditional methods.
“In the field of mechanobiology,” said Adie, "3D environments are really necessary in order to properly study the biological behavior and role of mechanical interactions between cells and their microenvironment.”
This technique, Adie said, will be useful in studying the interaction of cells—including migrating cancer cells—on their environment.
“Photonic force optical coherence elastography for three-dimensional mechanical microscopy.” Nichaluk Leartprapun, Rishyashring R. Iyer, Gavrielle R. Untracht, Jeffrey A. Mulligan & Steven G. Adie. Nature Communications 9, Article number: 2079 (2018).
Bonassar Group helps develop new cell therapy
NeoCart—a cell therapy that uses a patient’s cells grown in a collagen scaffold to repair knee cartilage defects—is in the final phase of a U.S. clinical trial thanks in part to research and development from the lab of Larry Bonassar, Daljit S. and Elaine Sarkaria professor of biomedical engineering and of mechanical and aerospace engineering.
Regenerative medicine company Histogenics announced an $87 million licensing agreement with biomedical technology firm Medinet to develop and distribute NeoCart in Japan. Bonassar said Cornell-based efforts played a significant role in the deal.
“We believe we have contributed to their having a really much more in-depth understanding of how their product works,” Bonassar said of Histogenics. “And I think that has been integral in their ability to, in this case, talk to the regulatory agencies in Japan as well as potential commercial partners there.”
NeoCart is produced by harvesting cartilage cells from the non-weight-bearing cartilage surface of the patient’s femur. The cells are expanded, embedded in a collagen scaffold and then incubated using a proprietary processor. One of the challenges for Histogenics was determining just how stiff the cartilage implant had to be to handle the wear and tear inside a knee joint.
“You can say, ‘It needs to be exactly what the native tissue is,’ but we know that’s not true,” said Bonassar. “But given that, how do we identify a threshold? How do you know when it’s ready?”
Through some novel testing methods, the Bonassar Group identified a mechanical transition point that occurs during the cell-culturing process. Gradually, the cells fill in the “sponge holes” of the scaffold so that it goes from porous to solid, Bonassar said.
“What happens when you take something with a bunch of holes in it and squeeze it? Those pores basically buckle,” he said. “But if you fill in the holes, eventually you’ll reinforce those pores so they don’t buckle. And we’ve been able to directly evaluate this process and demonstrate that if the pores are sufficiently full, you’ve reinforced the whole scaffold and it behaves differently.”
Histogenics’ sponsored research agreement with the Bonassar Group runs through 2019. Future goals include streamlining NeoCart’s manufacturing process using 3-D printing technology.
Immune-engineered device targets chemo-resistant lymphoma
The lab of Ankur Singh has partnered with researchers at Weill Cornell Medicine to explore how fluid forces may relate to the most common type of chemo-resistant lymphoma tumors’ drug resistance.
The team, which also included assistant professor of biomedical engineering Ben Cosgrove, has developed a “lymphoma micro-reactor” device that exposes human lymphomas to fluid flow similar to that in the lymphatics and parts of the lymph node.
In testing different subsets of diffuse large B-cell lymphoma (DLCBL), the group discovered that certain subsets, classified based on mutations in B-cell receptor molecules found on cell surfaces, responded differently to fluid forces. Most notably, the team discovered that fluid forces regulate expression levels of adhesion proteins known as integrins, as well as B-cell receptors.
The team found cross-talk between integrin and B-cell receptor signals that could help explain certain tumors’ drug-resistance.
“It is pretty remarkable that subclasses of the same tumor respond differently to mechanical forces,” said Singh. “If we can understand the role of all these biophysical stimuli, we may understand why some lymphomas are sensitive to treatment while others are refractory. Then we will be able to treat many more patients.”
“How Biophysical Forces Regulate Human B Cell Lymphomas.” F. Apoorva, Alexander M. Loiben, Shivem B. Shah, Alberto Purwada, Lorena Fontan, Rebecca Goldstein, Brian J. Kirby, Ari M. Melnick, Benjamin D. Cosgrove, Ankur Singh. Cell Reports 23 (2): 499-511 (2018).
Imaging tool could find early signs of arterial plaque
A brain imaging tool for neuroscience developed at Cornell could have unexpected benefits in research on another vital area of the body: the heart.
A research team led by Nozomi Nishimura, assistant professor of biomedical engineering, has applied multiphoton microscopy to the study of atherosclerosis—the buildup of plaque in the walls of the arteries. This buildup is a major cause of heart disease and stroke.
A descendant of the revolutionary two-photon microscopy born nearly 30 years ago in the Clark Hall laboratory of Cornell biophysicist Watt Webb, the Nishimura Group produced high-resolution images of the earliest evidence of plaque buildup—individual fat cells along the arterial wall—in mouse and human tissue samples.
“When you look at tissue under a microscope, there are a lot of indistinct features,” Nishimura said. “But to have something that is this bright, that shows something very specifically related to the disease, is pretty exciting. We believe it has a fair amount of clinical potential because of that specificity.”
Nishimura had previously worked with the lab of Chris Xu that produced high resolution in vivo images of neurons firing deep inside the brain of a mouse. These startlingly clear images, using three-photon microscopy (3PM) developed in Xu’s lab, got Nishimura thinking about other uses for the pioneering imaging technique.
One of the additional signals produced when using 3PM for imaging is third harmonic generation (THG), which detects the interface between materials that respond differently to light. Whereas most optical techniques require inserting a fluorescent dye molecule or protein—which absorbs laser light and then radiates it back out, usually changing the color—THG doesn’t require any dyes. The technique relies on the inherent properties of the structures being observed—for Nishimura’s work, fat deposits.
Nishimura sees potential for clinical application of this technique combined with emerging endoscopic technologies.
"Label-free imaging of atherosclerotic plaques using third-harmonic generation microscopy." D. Small, J. Jones, I. Tendler, P. Miller, A. Ghetti, and N. Nishimura. Biomed. Opt. Express 9, 214-229 (2018).
NOVEL Strategies to Fight pathogens
Metastatic breast cancer affects bone mineral before spreading An international collaboration led by Claudia Fischbach-Teschl—associate professor and co-director of the Cornell Center on the Physics of Cancer Metabolism—reports that not only does metastatic breast cancer favor a certain state of bone mineral, but that breast cancer tumors actually remotely enhance that favorable state—“talk,” in effect, with the region of choice—before metastasizing there.
“Cancer is not only about the cancer cells themselves, but also about in which context they actually develop,” Fischbach-Teschl said.
At the same time, this remote cellular interaction is taking place, the cancer cells are disrupting the bone’s natural turnover, a constant process in which old tissue is shed and new tissue forms. Metastasis in the bone triggers a vicious cycle: Cancer cells migrate to a region that’s suited for their growth, and their presence degrades the region, making it even more suited to tumor growth.
Gaining a greater understanding of the pre-metastatic niche, not only from a biological, but also a materials science perspective, could help inform therapeutic decisions in the future, Fischbach-Teschl said.
“The goal now is to really understand why these changes are happening,” she said. “Why and how do tumor cells change these properties in bone prior to the formation of metastasis, and how is that then functionally relevant to seeding a new tumor?”
"Multiscale characterization of the mineral phase at skeletal sites of breast cancer metastasis." Frank He, Aaron E. Chiou, Hyun Chae Loh, Maureen Lynch, Bo Ri Seo, Young Hye Song, Min Joon Lee, Rebecca Hoerth, Emely L. Bortel, Bettina M. Willie, Georg N. Duda, Lara A. Estroff, Admir Masic, Wolfgang Wagermaier, Peter Fratzl, and Claudia Fischbach. PNAS 114 (40): 10542-10547 (2017).
Sugar-coated vesicles prove effective in laboratory tests on deadly pathogens
Professors Dave Putnam and Matt DeLisa have joined forces with a group at Harvard Medical School to propose a better way to make conjugate vaccines for bacterial pathogens, including Haemophilus influenzae type b (Hib), a form of bacterial meningitis that kills thousands of infants annually in the underdeveloped world.
The method proposed by DeLisa and Putnam uses the versatility and ease of manufacture of outer membrane vesicles (OMVs), which the partnership has been developing for several years as a way to deliver targeted vaccines.
Animal models infected with two distinct and potentially deadly bacterial species—Staphylococcus aureus and Francisella tularensis—developed protective immunity against both when injected with the group’s OMVs.
In February, Cornell and Harvard jointly filed a provisional patent application for their OMV protocol.
“Immunization with outer membrane vesicles displaying conserved surface polysaccharide antigen elicits broadly antimicrobial antibodies.” Taylor C. Stevenson, Colette Cywes-Bentley, Tyler D. Moeller, Kevin B. Weyant, David Putnam, Yung-Fu Chang, Bradley D. Jones, Gerald B. Pier, and Matthew P. DeLisa. PNAS 115 (14): E3106-E3115 (2018).
"A single dose and long lasting vaccine against pandemic influenza through the controlled release of a heterospecies tandem M2 sequence embedded within detoxified bacterial outer membrane vesicles." Hannah C. Watkins, Catalina L. Pagan, Hannah R. Childs, Sara Posada, , Jose Rios, Cassandra Guarino, Matthew P. DeLisa, Gary R. Whittaker, David Putnam. Vaccine 35 (40): 5373-5380 (2017).