In-Depth Analysis of Metastatic Cancer Could Enable More Precise Treatments

Five hundred cancer patients are getting an in-depth look at their genomes as part of a new clinical study that is revealing some of the key molecular drivers of metastatic cancers. Some of the patients, who were diagnosed with more than 20 different types of cancer among them, are now working with their physicians to use their genomic information to guide treatment options.

The data are helping physicians match patients to clinical trials that address the precise DNA mutations that enable their cancers’ growth, says study coauthor Arul Chinnaiyan, an HHMI investigator and cancer biologist at the University of Michigan. He is among the first researchers to take this kind of precision medicine approach to better understand and treat metastatic cancers – an aggressive form of the disease in which cells from the original tumor break away and invade other tissues.

Chinnaiyan’s findings, published August 2 in the journal Nature, contribute to a growing body of research that reveals the molecular underpinnings of patients’ tumors. Chinnaiyan’s team has also made their dataset available to other scientists investigating metastatic cancer.

“Ninety percent of the time, metastatic cancer is the form of cancer that patients die of,” Chinnaiyan says. “It’s very difficult to treat once you have it.”

Caption: Arul Chinnaiyan’s team analyzed a variety of metastatic cancers throughout the body, including lung cancer (green) and breast cancer (pink). Credit: Alexander Tokarev

The ongoing clinical study employs tumor sequencing, in which researchers extract tumor cells from patients and characterize the cells’ genetic makeup. Using this information, Chinnaiyan and his team can create molecular profiles of the tumor that reveal details of what went awry – such as mutations, gene fusions (when two separate genes erroneously combine) and other molecular abnormalities. The data pointed Chinnaiyan and his team to five genes, all of which were commonly altered in patients with metastatic cancer. Additionally, the researchers observed that 12 percent of patients carried potential cancer-causing errors in DNA carried by sperm and egg cells.

“This gave us a pretty comprehensive picture of the molecular landscape of cancer,” said Chinnaiyan.

The data are a result of two genomic sequencing techniques – DNA and RNA sequencing, or whole-exome and transcriptome sequencing, respectively. In DNA sequencing, researchers extract and analyze DNA from a patient’s tumor and healthy tissues to try and discern what went wrong in the tumor. By comparing the two sets of DNA sequences, scientists can pick out genomic differences between the normal and the tumor DNA. “That's key because it allows us to potentially know what's driving the cancer in that individual patient,” Chinnaiyan said.

RNA sequencing allows researchers to better identify deleterious alterations, such as gene fusions or changes in gene expression. Chinnaiyan and his team also used RNA sequencing to analyze the amount and type of immune cells that infiltrated the patients’ tumor-invaded tissues. RNA sequencing data, he says, allows a clearer glimpse into the “immune phenotypes” associated with individual cancers – in other words, the factors that suppress the immune system’s ability to fight tumor growth.

“Immunotherapy has been one of the major areas of progress in cancer therapeutics, thus emphasizing the need to understand the immune microenvironment of the tumor,” Chinnaiyan explains.

He says that it’s crucial to understand that cancer is never static and always evolving – and treatments should reflect that. As tumors cross into different tissues, new mutations may arise, changing their molecular composition, which could diminish the efficacy of cancer drugs. Likewise, tumors can adapt to therapeutic drugs and develop new ways to survive. To maintain the most effective, up-to-date, treatment, Chinnaiyan argues that more frequent biopsies (of both the tumor and its immune microenvironment) are critical.

“We should be doing contemporaneous sequencing of cancer patients’ genomes – real-time assessments of the patient rather than relying on recommendations based on archival samples of the primary tumor,” he says.

Now, Chinnaiyan and his team are continuing to gather sequence data from patients with metastatic cancer. The researchers want to build and contribute to a large database for scientists and doctors to use. Chinnaiyan hopes that a genome-first approach will help doctors and patients develop agile treatment strategies that remain effective despite the dynamism of metastatic cancer.

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Dan R. Robinson et al. “Integrative clinical genomics of metastatic cancer,” Nature. Published online August 2, 2017, doi: 10.1038/nature23306.

Lessons from the Tarantula

Picture an organism the size of your hand, with a bristly body and eight bushy legs. Chances are, you’re thinking of a tarantula. As familiar as these shaggy arachnids are, it may surprise you to learn that they harbor a secret about human health: the muscles that control each spindly limb bear a remarkable molecular resemblance to the muscle beating in our chests.

For Christine Seidman, a human molecular geneticist and HHMI investigator at Brigham and Women’s Hospital and Harvard Medical School, that likeness gave her a new perspective on heart disease. Seidman studies a heart disease called hypertrophic cardiomyopathy (HCM). For those with HCM, the heart contracts too well, and does not relax properly, which increases energy consumption and leads to adverse events such as arrhythmias and heart failure.

Seidman’s past work has identified eight genes encoding for muscle proteins that, if mutated, cause HCM. Most commonly these mutations occur in two of the genes, one of which codes for myosin, a protein crucial to muscle contraction. The myosin-related mutations simply switch one amino acid for another during the protein-building process. These findings prompted a new question: “How could such a subtle change have such profound effects?” In search of an answer, Seidman looked beyond genetics.

During an HHMI science meeting in 2011, Seidman sought help from Raúl Padrón, a structural biologist at the Venezuelan Institute for Scientific Research (I.V.I.C.), whose journal articles she’d been following. At the time, Padrón was an HHMI international research scholar studying how muscle proteins interact in tarantulas (which he describes as “very friendly”).

“One of the critical proteins that Raúl was studying was – big surprise – myosin,” said Seidman.

Armed with the title of Padrón’s poster at the HHMI meeting, she set out to find him. Padrón recalls their first interaction in vivid detail: “I was in complete shock when Christine came to my poster; I had never met her before, and she was very well-known in my field, as she discovered many of the mutations we were mapping in the myosin model in our poster. She walked up to me and said ‘We need to work together to understand how different mutations affect the myosin motif.’”

And so, they did. Padron paired his expertise in structural biology with Seidman’s keen knowledge of genetics. Together with collaborators Lorenzo Alamo and Antonio Pinto, they investigated how HCM-associated mutations change the structural interactions of myosin that occur during cardiac relaxation.

As a geneticist, Seidman says it was beautiful to see the actual myosin structure, even at low resolution. “And there was another piece that was very important to me – Raúl could tell me the amino acids that participate in myosin interactions during relaxation.” It turned out that many of the amino acids involved in the molecular interactions that occur with relaxation are the very ones that are altered by HCM mutations. That, she said, was “an a-ha moment.”

Baby Venezuelan tarantula. Image credit: Raúl Padrón

Now, the two are planning next steps, asking the natural follow-up questions in their respective fields.

“We hope to take advantage of the ongoing ‘cryo-EM resolution revolution’ to achieve near-atomic resolution of myosin interactions by using this technique, which was actually invented by Humberto Fernández-Morán, a Venezuelan scientist working at Chicago University in 1966,” Padrón says. Seidman, too, hopes to continue structural analyses. “We’d very much like to work with Raúl to solve these structures using human specimens, with and without HCM mutations,” she says. “That would be a big step."

But the clinician side of Seidman hopes the information will help them answer a different question.

“We also want to know if there is a way to reduce the symptoms and adverse outcome that occur in HCM, by improving relaxation, with small molecules in the heart. In addition, we know that abnormal relaxation of the heart occurs in a lot of different diseases, not just HCM, so understanding if these structures might contribute to broader cardiovascular disease will also be very, very important.”

Janelia Turns 10

Seventeen years ago, at a restaurant in Boulder, Colorado, three scientists leaned over a table, deep in discussion about a sketch they’d just scribbled onto the back of a napkin. It didn’t show a biochemical pathway or molecular motif, but an idea for a facility where researchers could develop and access advanced technologies.

After three years of intense discussion and planning, this modest idea developed into a philosophical blueprint of an experiment that had the potential to shift the basic tenets of scientific research. The idea was a big one – a multimillion-dollar undertaking that would turn the traditionally siloed, grant-dependent approach to research on its head.

Working with distinguished architects, HHMI’s leadership began to chart physical, and cultural, plans for a building that could house their evolving “experiment.” By October of 2006, those plans became a reality, and the doors officially opened at HHMI’s first-ever independent research institute, Janelia Research Campus. The 700-acre institute focuses on imaging technology and neurobiology, tackling what HHMI Vice President and Janelia Executive Director Gerry Rubin calls one of the last frontiers of biology: the evolutionarily conserved mechanisms that underlie how the brain works.

Now, nearly 600 scientists, 1,050 publications, and 5 million cups of coffee later, the 10th anniversary of Janelia’s opening has arrived.

“We started as, and continue to be, an experiment in the social engineering of research communities,” says Rubin.

Back in 2006, Janelia’s launch garnered a lot of attention. Onlookers from academia met the new campus with raised eyebrows – some out of excitement, others out of skepticism. And underlying the attention and commitment was one clear question: Would it work?

“Our development is far from finished, but after 10 years, we’ve gained momentum and have found our footing in the scientific landscape,” says Rubin.

The past decade witnessed many scientific achievements and ushered in new mechanisms for fostering collaboration on an international level, such as the Visiting Scientist Program, and for facilitating open access to new technologies developed and built in-house, such as the Advanced Imaging Center. Now, as the campus continues to grow and evolve, new questions are emerging.

“We need to ask, how do we continue to challenge ourselves to do science that wouldn’t be done elsewhere? How do we get out of our comfort zone? Those questions are important in keeping momentum for any organization,” says Rubin. “It’s something we actively think about, and we want to reflect that in our choice of scientific problems and in how we approach them.”


Mapping the Connections

Ultimately, Janelia’s continuing evolution comes down to its community – scientists with insatiable curiosity and the gumption to pursue high-risk, high-reward research. 

Michael Reiser, a neurobiologist and group leader at Janelia, falls into that category.

Reiser, who joined Janelia in its early days, studies the neural pathways that give rise to animal behavior. His research centers on how the brain of the fruit fly – Drosophila – processes visual stimuli while the animal navigates its environment. Take, for instance, a fly that encounters an obstacle during flight and veers to avoid a collision. Reiser and his lab aim to help build a neurological map, or “connectome,” that shows the neuron-to-neuron connections that encode these visual cues – a tree or a wall, for example – and inform the fly to alter its route. But while the team works to contribute new pieces to the neural map, their main goal centers on interpreting and explaining the part of the connectome that senses obstacles, encodes the information, and ultimately, tells the fly to swerve. 

“Trying to understand the connectome is like solving multiple puzzles at the same time,” says Reiser. “There isn’t just one experiment that really nails down any one question. We have to attack this problem from all sides.”

Fortunately, Reiser has company. He is one of many Janelians, including physicist and group leader Harald Hess, who are working to generate a Drosophila connectome. Hess, unlike Reiser, doesn’t directly interfere with fruit fly flight patterns in search of understanding the neural mechanisms. He develops tools – microscopes that allow scientists like Reiser, and many others, to witness cells in their natural context, decipher their structural details, and even inspect the dynamic processes inside a single cell.

One instrument Hess developed that captures such minutiae is the focused ion beam-scanning electron microscope, or FIB-SEM. The microscope images extremely thin layers of a fly’s brain at high resolution and generates videos, akin to flip books, from hundreds of thousands of photos that reveal neuron-neuron interactions. The images result from a two-step process: The microscope’s ion beam shears off a few nanometers of tissue to expose a new layer of the brain, in much the same way a sandblaster would strip a layer of paint from a chair. With the new layer bared, the microscope takes a picture, and the cycle continues.

Hess describes Reiser as the “perfect customer” for the resulting videos – particularly those that reveal neurons in the visual system. Paired with genetic techniques that target specific neuron populations, the FIB-SEM images help Reiser and his team figure out the neural underpinnings of Drosophila behavior.

Hess believes that the fluid collaboration at Janelia is a boon to the campus’s research overall. “A major strength is not being too broadly committed,” he says. “At many other institutions you have to cover sample prep, and you need to be the surgeon, the microscopist, and the analyst. But here, there’s a comfort in knowing that I can focus on my own specialty, push that research to greater depth, and rely on other collaborators to likewise expand on their own research frontiers.”

Into the Cell

Hess and like-minded inventors at Janelia strive to push past the traditional constraints of microscopy, discovering new insights into areas like connectomics, subcellular organization, and live-cell imaging. But as with any progress in science, providing accessible information and resources to the greater scientific community is key.

Through Janelia’s Advanced Imaging Center, a selection of tools developed by Hess and fellow Janelia physicists benefit resident scientists and visitors alike.

Jennifer Lippincott-Schwartz, a group leader and cell biologist who recently moved her laboratory from the National Institutes of Health (NIH) to Janelia, has worked with Hess and his tools as both a visiting and a resident scientist. She describes their partnership as a two-way street. Hess and other close collaborators, such as group leader and Nobel Laureate Eric Betzig, ask Lippincott-Schwartz to try out new technologies and impart biologically relevant feedback. In turn, Lippincott-Schwartz approaches them with new cellular pursuits, inquiring about microscopes suited for her experiments.

In October 2016, the three researchers contributed to a paper in Science that provided new insights into one of the cell’s most prominent organelles (compartmentalized structures inside the cell, similar to internal organs in humans). Prior to the paper’s publication, scientists believed that this organelle, known as the endoplasmic reticulum, or ER, had a smooth, sheet-like appearance. Using Hess and Betzig’s custom-designed microscopes, Lippincott-Schwartz revealed that the true architecture of the ER involves tight, cross-linked tubular structures that create a flexible meshwork.

“With Eric’s microscopes we got close to getting our paper accepted, but the reviewers wanted to see electron microscopy too, which is not an easy shift if you’ve been doing a lot of light microscopy,” says Lippincott-Schwartz. “But we were able to work with Harald and the spectacular FIB-SEM and image the ER in a very short period of time. It turned out to be a tour de force of our paper.”

What’s more, the new understanding allowed Lippincott-Schwartz to build on an existing body of knowledge. Craig Blackstone and scientists at the NIH have shown that mutations in genes responsible for ER morphology are linked to spastic paraplegia in humans. The mutations cause malformation of the ER, which hampers the organelle’s ability to function properly in neurons, causing them to die. The resulting nerve damage leads to muscular dysfunction in the lower limbs. Lippincott-Schwartz’s paper suggested a link between the mutations and ER failure, and ultimately nerve cell failure, in the disease.

While the group’s paper does have medical implications, their fundamental objective as researchers and tool designers is not to hunt for treatments to neurological disorders. Likewise, for Reiser’s team – and Janelia as a whole – the goal of their research is not to cure brain diseases, but to help propel neuroscience as a field. The hope is to forge the groundwork that will empower medical advances and help physicians better understand, and therefore treat, neurological disorders in the future.

“A lot of what we do now is only possible because of the discoveries from 10, 20, or 50 years ago – discoveries made by people who didn’t realize their contributions would be relevant to real-world problems,” says Rubin. “We’re a medical institute, and I believe everything that we do will be medically relevant – maybe not for me, or for you, but perhaps for my seven-year-old granddaughter. It’s just a matter of time.”

A Place for Science in a Virtual World

By day, Janelian Christopher Bruns designs specialized software applications that give scientific images a new edge – or rather, a new dimension. With his apps, two-dimensional images become 3D graphics, allowing scientists to rotate and examine the images in greater depth. But come evening, when Bob's (Janelia Research Campus's on-site restaurant) turns from café to pub, Bruns veers from his day job into a different domain – virtual reality.

“Virtual reality has been a passion of mine for the past three years,” Bruns says. “When you put on a headset, you get this very engaging, even emotional, experience.”

Most people associate virtual reality, or VR, with the gaming sector; indeed that’s where Bruns got his start. In 2013 he developed software for the popular 90s video game “Doom,” casting users into an alien-ridden battleground for a more visceral thrill.  But beyond video games, Bruns sees the technology’s latent potential. “I have great hopes that virtual reality will be useful in scientific visualization,” he says. “But I do think it's appropriate to be skeptical – we’re still experimenting.”

Bruns explains that, early in his career as a structural biologist, it was fatiguing to decipher structures when he couldn’t tell which piece was in the foreground. “With 3D glasses, I could perceive depth, making the process more efficient and more comfortable.” Virtual reality could be the next step, he says. “In principle, you perceive all the same facts as you would on the monitor, but my hope is that VR can expedite the viewing, analysis, and understanding of already-solved molecules.”

A VR evangelist of sorts, Bruns sees recent widespread access to the technology as an opportunity to expand into a realm brimming with possibilities: Imagine a protein engineer who creates therapeutic compounds. Instead of designing a protein on a computer screen, the scientist could enter a virtual world, walk around the protein of interest, interact with it, and even make changes to amino acid sidechains.

What’s more, with the advent of motion-tracking controllers collaborators could connect on an entirely new level. Researchers separated by thousands of miles could potentially join the same simulated world, each seeing what the other is seeing, and even watching each other’s hand movements.

Bruns points out that virtual reality would not necessarily reveal new aspects of science, but rather, provide scientists a more effective visualization method. He compares it to when he was a structural biologist working with 3D stereoscopic displays (similar to how we view 3D movies).

Bruns has collaborated with his spouse, Cami K. Bruns, who earned a PhD in biology at Stanford University. Together, they've created software that displays molecules in a virtual realm, where users can “drive” around bonds and peer through benzene rings. His full vision, however, encompasses much more – VR-assisted drug development, protein engineering, and even an extension of his current work, which helps scientists trace neuronal pathways in mouse brains.

In the meantime, Bruns leads a band of virtual reality enthusiasts at Janelia, hosting demonstrations and tutorials. In-between demos, he’s working to produce the software that will enable VR-based scientific visualization. “Eventually,” he says, “when scientists at Janelia use it, we’ll be able to see if this is really going to be helpful or not.”

Dieting Device Tricks Brain into Feeling Full

In mid-January a novel obesity treatment surfaced in the public market. There are no constricting bands or rerouted intestines; the device hinges on the “feeling” of hunger—or lack thereof. Recently green-lighted by the FDA, the device, called the Maestro Rechargeable System, uses a pacemaker-like approach to curb appetite. It targets part of the body called the vagus nerve, which controls a handful of vital human functions, like heartbeat and breathing. But Entero Medics, producer of the device, focuses on its role as the hunger nerve, capitalizing on its ability to regulate brain-body satiety.

Doctors and researchers working with the Maestro System promote it as a new, safe and effective option in treating obesity. And though it’s an intriguing prospect, some clinicians grapple with the device’s feasibility as a practical option for most obese patients. For some, the sheer novelty is enough to be wary, but most concerns center on a hefty price tag and a modest weight loss.

But regardless of the system’s future, it’s the first FDA-approved obesity device since 2007 and a positive step in advancing obesity treatment and technology. Since the American Medical Association officially declared obesity a disease in 2013, researchers and patients are increasingly treating it as such, rather than a lack of self-restraint.

“It’s like having high blood pressure. You don’t blame somebody for having high blood pressure, you treat it,” says Susan Fried, Professor of Endocrinology, Diabetes and Nutrition at Boston University’s School of Medicine. “But we do blame people for being obese. I think people mistakenly assume it’s all environment since we can’t find one gene that’s responsible for obesity, and that’s not true.”

The Maestro Rechargeable System treats obesity with a surgically implanted chip paired with a battery pack and coiled portable charger. After a full charge, the device’s power lasts 2-3 days—which is more than most can say for their cell phones. But it’s the patient’s responsibility to keep a full charge as long as they have the device, which potentially, is the rest of their life.

Upon implantation, surgeons suture the device’s electrodes in a specific region of the lower abdomen, isolating the portion of the vagus nerve that innervates the stomach. These electrodes periodically send impulses into the nerve and block the signal from the stomach to the brain that causes the “hungry” sensation, hoodwinking the body into thinking that it’s full.

This electrical strategy is known as VBLOC therapy (vagal blocking therapy), and though stimulating the vagus nerve to improve health isn’t a new concept, doctors don’t fully understand how these electrical pulses stop vagal communication. They do, however, know that complete blockage of the vagus nerve is ineffective. Other mechanisms in the body recognize the loss of appetite signal and attempt to compensate for the deadpan nerve. That’s why the device works in pulses instead of one giant electrical blockade.

But the pulses aren’t the same for everyone—every patient has a different pulse-to-weight-loss ratio, and the trick is striking the right balance. During the clinical trials, doctors monitored patients’ weight loss closely, tailoring millivolts to best elicit feelings of fullness.

“The pulses aren’t random. They’re dependent on the patient,” says Dr. Caroline Apovian, Director of Nutrition and Weight Management Center at Boston Medical Center. “Patients follow up with their doctors to hit the sweet spot of pulse generation,” she adds. After doctors insert the device, they tune each patient’s electrical impulses based on how hungry they feel. Descriptors vary, but doctors monitor patients for feelings of fullness, pressure and heartburn to gauge satiety.

Under the umbrella of bariatric surgery, the Maestro Rechargeable System is the safest, but is most modest in weight loss. Over a one year period in a clinical trial called ReCharge, patients with the device lost an average of 9.6% of their total body weight. For contrast, the gastric bypass, currently the “gold standard” of bariatric procedures, stands out for its dramatic weight loss effects—around 33% of total body weight. But in terms of safety and post-surgery complications, the Maestro System is the better option.

“This surgery is quite possibly the safest thing we have right now,” says Dr. Sanjani Shah, Assistant Professor of Surgery at Tufts University School of Medicine. “It’s completely reversible—we’re not cutting or pasting anything. There’s nothing being rerouted.”

During the ReCharge trial, less than 4% of the 233 patients enrolled experienced severe problems ending in re-hospitalization or removal of the device. For the most part, patients who did report side effects complained of moderate ailments like bloating, nausea or upset stomach. But for some, like local Boston patient, Mike Magnant, the device seems virtually flawless.

“I’ve not been nauseous, no headaches, never felt dizzy. I don’t have any restrictions on what I can eat,” Mike says.

After hearing an ad for the Maestro System on the radio, Mike enrolled in Entero Medics’ first clinical trial. He fit the criteria: between 18 and 65 years old, unsuccessful long-term weight loss in other structured programs, and a Body Mass Index between 35 and 45 kg/m2 (between 260 and 330 lbs for a 6-foot male adult). After having the device for three years, Mike says he wouldn’t give it back even if the FDA hadn’t approved it.

“To lose 70 pounds and not gain it back? There are so many benefits to losing that weight, and to me, the best part is keeping the weight off,” he says. “This is forever for me.”

The patients from the Maestro System’s clinical trials have, on average, maintained the weight lost. But the trials are still in relatively early stages, and only time can tell if the system will prove effective over a lifetime.

While Mike’s experience is successful, it’s not necessarily representative of all patients with the device. Some doctors speculate that VBLOC therapy may be more of a fad than an emerging go-to in obesity treatment. Dr. Lee Kaplan, Associate Professor of Medicine at Harvard and Director of the Massachusetts General Hospital Weight Center, puts it in perspective when he points out the patient-to-patient variation that inevitably comes with any disease treatment. In this case, patients that receive the device have no way to tell if their weight loss will be above, below, or on par with the average.

“What we really need is a parameter predicting how well the person may do with the device, but as of now we have no evidence for that,” says Dr. Kaplan. “So the question is, ‘Is it the best idea to use this device, which requires surgery?’ I think it’s going to be a hard sell, given the cost.”

Though Entero Medics hasn’t landed on a price or whether insurance will cover part or all of the cost, speculative prices hover around $15,000-$30,000. In considering the device’s relatively slight results, some patients may find it too expensive. But Entero Medics highlights the safety and sustainability of weight loss as key players in their future push to market.

Currently, doctors and researchers are continuing to follow patients with the device in a five-year, post FDA-approved study to monitor sustained and continued weight loss and any complications that may surface.

Looking forward, Dr. Shah hopes the Maestro Rechargeable System continues to gain attention from the public as an option for obesity treatment. “I’d be really happy if it got out in the public eye and patients understand the option—to say hey, this is a great other option if you’re considering surgery in morbid obesity.”

Fluorescent Tumors - Cutting on the Glowing Line

For decades cancer surgeons have had two tools with which to guide their scalpel: their hands and their eyes. Surgical tumor removal is the cornerstone of many cancer therapies, but in 20-50% of patients, microscopic scraps of cancerous tissue are accidentally left behind, and eventually, the tumors return. During surgery, it’s been virtually impossible to know if the entire tumor has been removed — until now.

Recent clinical research at the University of Pennsylvania is zeroing in on a technique that allows surgeons to more precisely define the boundary between cancerous and noncancerous tissue by making tumors fluoresce.

Before surgery, doctors inject a dye into the bloodstream, known as indocyanine green, or ICG, and wait about 24 hours for the dye to accumulate within the tumor. Because tumors grow so quickly, they stretch and develop “leaky walls,” allowing ICG to infiltrate and collect in the tumor. After the dye seeps into the tumors, doctors use a near infrared, or NIR, imaging system to image the cancerous tissue, which glows green on the surgeon’s computer screen. This fluorescence allows surgeons to remove tumors more accurately and helps limit the traces of post-surgery cancer.

The study, led by Dr. Sunil Singhal and David Holt, and surgical professor at UPENN, was published in PLOS ONE.

After researching the fluorescence methods in mice and dogs, five patients in a clinical trial were treated using ICG and the NIR imaging system. In all five cases, the tumors fluoresced onscreen, showing the efficacy of this technique in humans. In one of the four patients, the tumor seemed to be located clearly in one part of the lung; the rest of the lung looked and felt normal according to doctors and pre-surgical tumor scans. But under NIR light, parts of the lung still fluoresced.

“We initially thought there was a problem with our machine,” said Holt. “But it turns out, that patient had diffuse microscopic cancer.” Confirmed by biopsy, the patient received proper treatment and survived.

But there are still a few issues to work out. The ICG-NIR imaging technique was unable to distinguish between noncancerous inflamed tissue and cancerous tumors. If normal tissues are inflamed, chances are they also have leaky vessels, allowing dye to collect, just as it collects in tumors. In future research, Holt hopes that tumor-specific dyes can be used to differentiate and avoid confusion between noncancerous inflamed tissue and cancer.

Map My Brain

With every smell, memory, or flicker of emotion, tangled pathways of electrical activity light up in our brains and process the information, creating a concise impression of a world photoshopped by our neurons.

But these neuronal pathways don’t line up in a simple, linear transfer of information — there are trillions of synapses, and only recently have researchers really begun to dive into the extensive connections.

Each circuit is an intricate wiring of neurons that transmits signals through an electrical patchwork. Ultimately, every human function comes down to these “wiring diagrams” — maps of specific neuron connections that promote proper brain function.

Neuroscience is starting to move away from more traditional studies, like that of neuron structure or general functions in areas of the brain, and is shifting toward tracking connectivity. Scientists are trying to fill in the middle ground, to untangle the brain’s highly complex neural circuitry, and ultimately lay it out in a decipherable map.

Researchers are tweaking their techniques, incorporating elements of bioengineering and computational optics to expand the realm in which they can study the neuron and its connections in the brain. Some researchers have adapted Nobel-prize winning super resolution microscopy to scrutinize tiny details of neurons that were previously undistinguishable. Scientists hope that eventually these techniques can compile a new foundation for understanding cognition and mental health.

“Figuring out how the neurons come together to make these circuits is a big, rapidly advancing area of neuroscience today,” says Joshua Sanes, Harvard professor and researcher at Harvard’s Center for Brain Science. “Our motivations come from the fact that [neurons] underlay all brain activities, and that there are some psychiatric diseases that are suspected to occur through mis-wirings in the brain.”

In 2007, Sanes helped neuroscience reach a colorful breakthrough. Jeff W. Lichtman, Harvard professor of neuroscience and researcher at Harvard’s Center for Brain Science, and Sane’s research teams developed a technique known as Brainbow, a part of the Center’s Connectome Project.

Meant to tease apart the long tracks of neurons in the brain, the Brainbow method individually labels neurons with fluorescent proteins. These proteins express up to 100 different colors at a time, bringing colorful order to what was once an indiscriminate glob of neurons.

Sanes compares it to the wirings of a computer. All of the wires need to be accounted for and correctly connected, especially the ones involved in complicated circuits. Neurons are a lot like that, there are long “wires” that come from the bodies of neurons called axons and dendrites, and they hook up with other neurons to make precise patterns of connectivity. But if the wires aren’t correctly connected, the neural message gets distorted and can lead to mental deterioration.

“Having the wires in different colors lets you trace them and see where they go,” says Sanes. Currently, he and other scientists are building off of this colorful map to develop other research techniques that help chart connections in the brain.

Outside of the Connectome Project, other researchers at Harvard like Adam Cohen, professor of chemical biology and physics, and Venkatesh Murthy, professor of molecular and cellular biology, are using stimulation techniques to activate neurons and study their response in real time. Cohen has engineered a technique in which the neuron itself is able to make a protein that lights up to indicate electrical activity, and this light can then propagate through circuits of up to 100 neurons.

“The particular trick that Adam Cohen’s lab did is a phenomenally rational and beautiful design,” says Murthy. “It’s one of the best forms of this type of indicator.”

The light-up protein is called “Optopatch” and when engineered to a neuron, can be stimulated by a particular kind of light. This light activates the electrical impulse, and researchers can watch as Optopatch’s red glow fluoresces outwards, highlighting the signal’s path.

Murthy hopes to use this light-up pathway to help track neurons and even map the neural counterparts of particular smells.

While Murthy and Sanes aim to decipher larger neural circuits in the brain, researchers like Jan Tonnesson, at the University of Bordeaux, are taking a more detailed approach, zooming in on intricacies of the neuron that, until recently, have never been seen before. Tonnesson and his colleagues have applied the Nobel-prize winning microscopy technique called STED, more commonly known as super resolution microscopy, to study tiny details of the neuron — specifically, miniscule spines that extend from one neuron to the next, making the synapses that create the connections Sanes and Murthy are interested in studying.

“It opens up a completely new world for us,” says Tonnesson.

Super resolution microscopy allows researchers to clearly see images up to four times smaller than other microscopy techniques, and Tonnesson is taking advantage of that, exploring the microcosms of single neurons.

He and his colleagues at the University of Bordeaux stimulate each spine as if by another neuron and use the super resolution to gather data on how each spine responds individually to the contact. A single neuron may have thousands of spines, and while each spine is independently contacted, the total stimulation is what elicits a signal down the neuron, potentially propagating a circuit.

Tonnesson recognizes that, while super resolution is new to neuroscience, it offers a new angle in analyzing neurons and how neuronal structures may affect proper signal sending.

“We should treat a lot of this as on-going, moment-to-moment innovation,” says Murthy. “None of this is the final product, and I think part of the excitement is simply that we’re seeing what is possible. Sure, there are specific things that we are discovering now, but they’re opening doors to many more things in the upcoming decades.”