BME Magazine: Fall 2019

FALL 2019 DukeBME
MAGAZINE

BIOMEDICAL ENGINEERING AT DUKE UNIVERSITY

Engineering Biology for Medicine

inside: The Body on Defense 8 Big Ideas on a Small Surface 12 The Evolution of Genetic Engineering 26



Duke BME Magazine is Contents
published twice yearly by Duke
DUKEBME MAGAZINE | BIOMEDICAL ENGINEERING AT DUKE UNIVERSITY
Biomedical Engineering.
FEATURES
Mailing Address:
Room 1427 2 Letter from the Chair

Fitzpatrick Center (FCIEMAS) 3 Duke BME by the Numbers
101 Science Drive
4 Engineering Biology for Medicine
Campus Box 90281
Durham, NC 27708-0281 A new conference hosted by Duke BME, Nature Medicine and Nature Biomedical
Engineering provided a snapshot of the most exciting work across different areas
P: 919-660-5131 of research within bioengineering, and conveyed the promise of the field for
bme.duke.edu improving health

Editorial Director: 8 Engineering the Immune System
Ashutosh Chilkoti
Joel Collier and his lab harness nanomaterials to aid the body’s natural defense
Editor: system
Michaela Kane,
Duke BME Communications 10 Engineering Mechanics for Medicine

Art Director: As pioneers in the new field of mechanobiology, Brenton Hoffman and his lab
Lacey Chylack, investigate how mechanical forces can shape and control living cells
Phase 5 Creative, Inc.
12 Engineered Tissues for Medicine
Photo credits by page:
Jonathan Lee: George Truskey and Shyni Varghese use innovative lab-on-a-chip technologies to
create much-needed models for tissues, organs and diseases
Table of Contents
Megan Mendenhall: 16 Engineering the Brain
Inside front cover, 2, 19
Michaela Kane: 4,5,6,7, With novel approaches to studying neurons, Yiyang Gong and Michael Tadross
seek to understand the body’s most complicated organ
back inside cover
Collier Lab: 9 20 Engineering Microbes for Medicine

Les Todd: 10, 12, 13, 14, 20, With work spanning gene circuits, antibiotic resistance and the mathematical
25, 26 modeling of cellular networks, Lingchong You explores how to harness microbes
for medical purposes
Tadross Lab: 17
Jared Lazarus: 23 22 Engineering Microenvironments for Medicine

ON OUR COVER: Nenad Bursac and Tatiana Segura are engineering hydrogel microenvironments to
Julia Kuhl, Pratiksha physically and chemically support the growth of skeletal muscle and brain tissue
Thakore and LaurenToth,
Hoffman Lab, Bursac Lab, 26 Engineering the Human Genome
Pratiksha Thakore and
LaurenToth, Hoffman Lab, Charles Gersbach discusses his pioneering work with CRISPR and the future of
Elias Sideris, Chelsea Fries, this ground-breaking technology

You Lab.

LEFT: The interior of
the Fitzpatrick Center
for Interdisciplinary
Engineering, Medicine
and Applied Sciences,
home to Duke BME.

A CONFERENCE TO REMEMBER


Dear Colleagues and Friends, of mechanobiology, novel approaches to mapping
the human brain, and features about work at the
Good work is rarely accomplished alone. intersection of tissue engineering and regenera-
For me, the 2019 Engineering Biology tive medicine.
for Medicine conference served as an
energizing reminder that breakthrough discov- Our faculty are just one of the reasons Duke
eries often emerge due to collaborations at the BME is consistently ranked among the best
intersection of engineering, biology and medicine. biomedical engineering programs in the United
States, and I’m thrilled with the opportunity to
It was wonderful to welcome colleagues from highlight what is just a small fraction of their
schools as far-flung as Berkeley, Chicago, Co- excellent research. Duke BME has blazed an ex-
lumbia, Cornell, Georgia Tech, Harvard, Hopkins, citing trail in the last fifty years, and I know there
MIT, UCSF, Yale, and ETH Zurich to Duke BME for is more innovative work on the horizon.
the May 2019 conference, which was co-spon-
sored by Nature Medicine and Nature Biomedical Ashutosh Chilkoti
Engineering.
Chair
With sessions covering topics that spanned Duke Biomedical Engineering
mechanobiology, synthetic and systems biol-
ogy and immune engineering, this event was a
wonderful opportunity for leading researchers to
highlight successful research, and discuss how
their work could solve long-standing problems
within the biomedical field.

I was thrilled to have several Duke BME faculty
among the speakers presenting their own work
and introducing sessions. In our newest issue of
the Duke BME Magazine, we take a deeper look
at their impressive research, with stories about
researchers using lab-on-a-chip technologies to
study diverse diseases, work in the emerging field

2 | DUKEBME Magazine















ENGINEERING MECHANICS FOR MEDICINE

UNDERSTANDING

Cells Under Pressure

Brenton Hoffman’s lab explores how mechanical forces can shape and control our cells

Most researchers today understand ogy that can’t be solved through chemistry alone.
biology through the principles When you apply a force on a cell, that pressure
of chemistry. Cells can commu­
nicate through chemical signals, can alter and control its structure and behavior.
and traditional medicine has For example, the force generated by blood flow
long focused on how to treat disease by modifying pushes on the cells in blood vessels, helping them
those signals. But according to Brenton Hoffman, grow into the correct shape and behave normally.
an assistant professor of biomedical engineering at The same principle, Hoffman says, can be ap­
Duke University, this approach is incomplete, as it plied to a disease like breast cancer.
ignores a major factor in
cell biology: physics. “A breast tumor is normally discovered when
“Today, when we get someone fells a lump, and we know that a lump
“If we can understand the sick we usually get a pill is a local increase in stiffness, which means it’s a
pathological mechanics, that will affect our chem­ mechanical input to cells,” says Hoffman. “As we
learn more about these mechanical inputs, we’re
we can control, or ical system,” says Hoff­ examining whether the physical changes in cells
man. “But if you look and their local environments that make cancer­
maybe eliminate, the diseases that lack a clear ous tissue stiff may actually be a trigger for cancer
to spread, just like if you have a perturbed growth
pathological signaling chemical treatment op­ factor or a mutated receptor.”
tion, like cancer, asthma,
that drives mechano- cardiovascular disease, Until recently, researchers had no way to ex­
sensitive disease.” or muscular dystrophy, plore how these processes worked, but the Hoff­
man lab has circumvented this problem by creat­
they all have a mechan­ ing tunable protein sensors capable of measuring
ical component that forces inside living cells. These tension sensors
hasn’t previously been contain a specially engineered module that emits
looked at.” a fluorescent glow under normal conditions, but
Hoffman is pioneering dims if it experiences a change in force. The sen­
the new field of mecha­ sor is placed inside specific proteins that physi­
nobiology, which is the cally connect the cell to its surroundings. When
study of how physical these proteins feel a physical force, they stretch,
forces affect cell behavior. causing the sensor to dim.
His lab explores how the
chemical and mechanical “You could argue that we’re making the tools
aspects of biology inter­ to do basic studies, but that’s necessary, especially
act, and how researchers in a newer field,” says Hoffman. “If we can under­
can use mechanics to study what he calls mecha­ stand the pathological mechanics, we can control,
no-sensitive diseases and address problems in biol­ or maybe eliminate, the pathological signaling
that drives mechano-sensitive disease.” n

10 | DUKEBME Magazine





















the door open for the antibiotic to kill the patho­ wonder how can we do something like this?” The image shows
genic cells. Once the antibiotic-resistant plasmids In one project, You and colleagues engineered fluorescent bacteria
are gone, the synthetic ones become inactive. bacteria such that they spontaneously grew into encapsulated in alginate
“This is one example of synthetic biology where dome shapes. When provided with gold nanopar­
beads. This process has
we designed a genetic program to control cell be­ ticles, the bacteria incorporated them into the been used by the You
havior,” You says. structures. The researchers then used a pair of lab to generate living
He is working on several other aspects of an­ these conductive domes to create a pressure sensor functional materials
tibiotic resistance as well. In collaboration with in an electrical circuit.
Deverick Anderson, an infectious disease physi­ “This is the first time anyone has built a struc­ for versatile bio-

manufacturing.
cian in the Department of Medicine, he described ture in a predictable manner using living cells that (Credit: You Lab)
the dynamics of a microbial community that is carry out a specific function,” You says.
resistant in the face of antibiotic treatment, and You’s research projects may seem wide-ranging,
compared that to the dynamics in
a “resilient” community—one that
appears to be resistant but is not. “Nature gives us all these living functional materials.
The researchers showed in the lab I grew into this shape from a single cell. If you think

how a resilient community can be about that, it’s quite amazing. As an engineer, I
knocked out with first-line antibi­ wonder how can we do something like this?”
otics by using a customized strategy
of timing and dosing.
You is also active in another branch of synthet­ but they are all driven by the same questions: how
ic biology—programming microbes to build pat­ do microbial communities behave in space and
terns or structures. “Look at nature,” he says. “Na­ time, and how can those behaviors be modified?
ture gives us all these living functional materials. I “Deep down I’m very curious,” You says. “It’s
grew into this shape from a single cell. If you think incredibly, incredibly fascinating to me—all of
about that, it’s quite amazing. As an engineer, I this.” n

Fall 2019, Issue 1 | 21

ENGINEERING MICROENVIRONMENTS FOR MEDICINE

FIXING

Muscle and the Brain

Nenad Bursac and Tatiana Segura are engineering hydrogel microenvironments to physically
and chemically support the growth of skeletal muscle and brain tissue | By Ken Kingery

ABOVE: A stained With the number of times the word promptly solidify to provide a crucial three-dimen­
cross section of the “gel” comes up in the research of sional scaffolding for cells to organize and grow.
new muscle fibers. Nenad Bursac and Tatiana Se­ And by adding the perfect combination of growth
The red cells are gura, one would be forgiven for factors, enzymes, nutrients and supporting cells,
striated muscle thinking they might work in the their laboratories are successfully “engineering”
fibers, the green haircare or running shoe industries. Their gels, some of most challenging human tissues, including
areas are receptors however, are aimed at much more difficult tasks skeletal muscle and brain matter.
for neuronal input, than holding hair styles or cushioning feet.
and the blue patches In 2014, Bursac and his team were the first to
are cell nuclei. Bursac and Segura, both professors of biomed­ grow human skeletal muscle that contracts and
(Credit: Bursac Lab) ical engineering at Duke University, are two of responds just like native tissue to electrical pulses,
the leading researchers working to grow function­ biochemical signals and pharmaceuticals. While
al tissues both inside and outside of the human this initial success required a muscle biopsy to
body. While the gels being engineered in their lab­ isolate and grow human “almost muscle cells”
oratories are initially more liquid than solid, they called myoblasts, they soon demonstrated the abil­

22 | DUKEBME Magazine

“...muscle cells derived from
induced pluripotent stem
cells form muscle fibers that
contract and react to electrical
and biochemical stimuli
mimicking neuronal inputs,
just like native muscle tissue.”

ity to achieve similar results starting from cellular es for future studies and individualized health care.
scratch—human induced pluripotent stem cells. “The prospect of studying rare diseases is espe­

The method took years to develop, with the cially exciting for us,” says Bursac. “When a child’s
researchers making educated guesses and taking muscles are already withering away from some­
baby steps toward their goal. The difference-maker thing like Duchenne muscular dystrophy, it would
was their unique cell culture conditions and 3-D not be ethical to take muscle samples from them
matrix, which allows the cells to grow and develop and do further damage. But with this technique,
much faster and longer than the 2-D approaches we can just take a small sample of non-muscle tis­
that are more typically used. sue, like skin or blood, revert the obtained cells to

In the 2018 study, Bursac and his ABOVE: Nenad
group showed that after two to four Bursac
weeks of 3-D culture, muscle cells de­
rived from induced pluripotent stem LEFT: A cross
cells form muscle fibers that contract section of a muscle
and react to electrical and biochemical fiber grown from
stimuli mimicking neuronal inputs, induced pluripotent
just like native muscle tissue. stem cells. The green
indicates muscle
The pluripotent stem cell-derived cells, the blue is cell
muscle fibers also develop reservoirs nuclei, and the red
of “satellite-like cells” that are nec­ is the surrounding
essary for normal adult muscles to support matrix for
repair damage and regenerate, while the cells.
the muscles made using muscle bi­ (Credit: Bursac Lab)
opsy had much fewer of these cells.
The stem cell method is also capable Fall 2019, Issue 1 | 23
of growing many more cells from a
smaller starting batch than the biop­
sy method.

Both of the advantages point to­
ward a possibility of using this new
method for regenerative therapies
and for creating models of rare diseas­

ENGINEERING MICROENVIRONMENTS FOR MEDICINE

“We have something that is working, and place an entire body’s worth of
diseased muscle, it could be used
hopefully we can now figure out the in tandem with more widely tar-
mechanisms for that improvement, because geted genetic therapies or to tar-
get more localized muscle repair.
that is what leads to new engineering.” In Segura’s laboratory, re-

searchers are focusing on repair­
a pluripotent state, and eventually grow an endless ing perhaps the most stubborn organ in the hu­
amount of functioning muscle fibers to test.” man body—the brain.
The technique also holds promise for being The brain has a limited capacity for recovery after
combined with genetic therapies. Researchers stroke and other diseases. Unlike some other organs
could, in theory, fix genetic malfunctions in the in the body, such as the liver or skin, the brain does
induced pluripotent stem cells derived from a pa­ not regenerate new connections, blood vessels or
tient and then grow small patches of completely new tissue structures. Tissue that dies in the brain
healthy muscle. While this could not heal or re­ from stroke is absorbed, leaving a cavity, devoid of

24 | DUKEBME Magazine

FAR LEFT: The image
shows hydrogel that
was injected into the
stroke core. Axonal
filaments are shown
in red, astrocytes are
dyed green, nuclei
appear blue and the
hydrogel is white.
(Credit: Elias Sideris)

LEFT: Tatiana Segura
with graduate student
Katrina Wilson.

blood vessels, neurons or axons, the thin nerve fibers in scars and impedes regrowth of functional tissue.
that project from neurons. After 16 weeks, the stroke cavities contained re­

In a recent study conducted with mice, Segu- generated brain tissue, including new neural net­
ra sought to coax the healthy tissue surrounding works—a result that had not been seen before. The
the cavity into healing the stroke injury. She en- mice with new neurons also showed improved mo-
gineered a gel to inject into the stroke cavity that tor behavior, though the exact mechanism wasn’t
thickens to mimic the properties of brain tissue, clear.
creating a scaffolding for new growth.
“We have something that is working, and hope­
This artificial material creates an environment fully we can now figure out the mechanisms for
that helps local, native stem cells do their best work that improvement, because that is what leads to
to promote healing—providing the physical struc­ new engineering,” says Segura. “If you can discov­
ture as well as the biological cues that encourage er which pathways are causing the improvements,
cells to grow. For example, the gel is infused with then there are molecules you can deliver to engage
molecules that stimulate blood vessel growth and those pathways more directly and hopefully lead to
suppress inflammation, since inflammation results a therapy that will act faster and more robustly.” n

Fall 2019, Issue 1 | 25

ENGINEERING THE HUMAN GENOME

The Evolution

of Genetic Engineering


A Q&A with Charles Gersbach

Charles Gersbach, the Rooney Family Associate Professor of Biomedical Engineering at Duke
University, leads a lab that is centered on developing and applying genome engineering
tools––most notably CRISPR-based technology. CRISPR-Cas is a bacterial defense system
that allows bacteria to use RNA molecules and CRISPR-associated (Cas) proteins to target
and destroy the DNA of invading viruses. The discovery of this technique sparked a genome
editing revolution as researchers explored how the tool could be used to specifically target
and edit DNA in human cells. In the years since its discovery, Gersbach and his lab have
used this technology to study genetic diseases like Duchenne muscular dystrophy, precisely
control gene expression and even develop tools that can make CRISPR more accurate.

Cartoon crystal How did genetic engineering come to be research or musculoskeletal research, or stuff
structure of the your area of research? pertaining to diabetes or neurological work. All of
TALEN gene editing I knew that I wanted to go down an academic ca- these topics essentially involved trying to get cells
technology. reer path where I could help advance regenerative to do something interesting. As a very simplified
(Credit: Gersbach Lab) medicine and gene and cell therapies. I wanted to example, if we want cells to behave like cartilage
work on something that could affect a lot of dif­ cells, we essentially bang on them using mechani­
ferent areas within bioengineering, and I realized cal force and hope that they turn on the cartilage
that gene expression was a central component of a genes, and if we want cells to behave like neurons
variety of research. we electrically shock them and hope that kicks
the neuronal genes into gear. In all these cases
There were different wings in the building you’re applying external stimuli and hoping that
where I worked in graduate school, each focused internally the right genes get expressed. If the goal
on regenerative medicine as it related to a particu­ across all of these areas is to get the right genes on
lar organ system. In different parts of the build- and off, I was curious if there was a better or more
ing, you could look at posters for cardiovascular
direct technology to go in and program
gene expression.

CRISPR is a relatively new technol-
ogy. How did that end up being the
focus of your lab’s work at Duke?
The first paper that described using
CRISPR in human cells was published
in 2013, so we were working with
technologies that preceeded it. The first
was engineered zinc finger proteins,
which could be used to modify a spe­
cific region of the genome. At the time
people were using zinc fingers to make

26 | DUKEBME Magazine