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On-the-Spot Gene Readouts Offer Clues to How Cells Work

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Credit: MIT and Harvard Medical School, Cambridge, MA

Just as two companies can merge to expand their capabilities, two technologies can become more powerful when integrated into one. That’s why researchers recently merged two breakthrough technologies into one super powerful new method called ExSeq. The two-in-one technology enables researchers for the first time to study an intact tissue sample and track genetic activity on the spot within a cell’s tiniest recesses, or microenvironments—areas that have been largely out of reach until now.

ExSeq, which is described in a paper in the journal Science [1], will unleash many new experimental applications. Beyond enabling more precise analysis of the basic building blocks of life, these applications include analyzing tumor biopsies more comprehensively and even unlocking mysteries of how the brain works. The latter use is on display in this colorful cross-section of a mouse’s hippocampus, a region of the brain involved in the memory of facts and events.

Here you can see in precise and unprecedented detail the areas where genes are activated (magenta) in the brain’s neurons (green). In this particular example, the genes are working within subregions of the hippocampus called the CA1 and dentate gyrus regions (white, bottom and top left).

ExSeq is a joint effort from NIH grantees Ed Boyden, Massachusetts Institute of Technology (MIT), Cambridge, and George Church, Harvard Medical School, Boston. The new method combines a technology called tissue expansion with an in situ sequencing approach.

Tissue expansion swells the contents of tissue sections up to 100 times their normal size but retains their same physical structure [2]. It’s sort of like increasing the font size and line spacing on a hard-to-read document. It makes cellular details that were outside the resolution range of the light microscope suddenly accessible.

With the information inside cells now easier to see, the next step involves a technique called FISSEQ (fluorescent in situ sequencing), which generates readouts of thousands of mRNA molecules in cells [3]. FISSEQ works by detecting individual RNA molecules where they are inside cells and amplifying them into “nanoballs,” or rolled-up copies of themselves. Each nanoball can be read using standard sequencing methods and a fluorescence microscope.

Using the combined ExSeq approach, the team can analyze precisely where gene activity changes within tiny cellular microenvironments. Or, it can compile a more-comprehensive readout of gene activity within cells by analyzing as many gene readouts as detectable. When used in the hippocampus, this untargeted, “agnostic” approach led to some surprises—revealing unusual forms of RNA and, by association, genes for proteins not previously linked with communication between neurons.

Like many technology developments, the scientists envision that ExSeq can be used in many ways, including for more precise analysis of tumor biopsies. To illustrate this point, the researchers analyzed breast cancer metastases, which are cells from breast tumors that have spread to other areas in the body. Metastases contain many different cell types, including cancer cells and immune cells.

Using ExSeq, Boyden and Church learned that these distinct cell types can behave differently depending on where they are inside a tumor. They discovered, for example, that immune B cells near tumor cells expressed certain inflammatory genes at a higher level than immune B cells that were further away. Precise information about a tumor’s composition and activity may lead to development of more targeted approaches to attack it.

Many discoveries come on the heels of transformative new technologies. ExSeq shines a much brighter light on the world of the very small. And that should help us better understand how different parts of cells work together, as well as how cells work with each other in the brain, in cancer, and throughout the body.


[1] Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Alon S, Goodwin DR, Sinha A, Wassie AT, et al. Science. 2021 Jan 29;37:eaax2656.

[2] Expansion microscopy. Chen F, Tillberg PW, Boyden ES. Science. 2015;347:543-548.

[3]. Highly multiplexed subcellular RNA sequencing in situ. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, et al. Science. 2014;343:1360-1363.


Ribonucleic Acid (RNA) (National Human Genome Research Institute/NIH)

Synthetic Neurobiology Group (Massachusetts Institute of Technology, Cambridge)

George Church (Harvard Medical School, Boston)

NIH Support: National Human Genome Research Institute; National Cancer Institute; National Institute of Biomedical Imaging and Bioengineering; National Institute of Mental Health; National Institute of Neurological Disorders and Stroke

Welcoming First Lady Jill Biden to NIH!

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Video Event

It was wonderful to have First Lady Jill Biden pay a virtual visit to NIH on February 3, 2021, on the eve of World Cancer Day. Dr. Biden joined me, National Cancer Institute (NCI) Director Ned Sharpless, and several NCI scientists to discuss recent advances in fighting cancer. On behalf of the entire NIH community, I thanked the First Lady for her decades of advocacy on behalf of cancer education, prevention, and research. To view the event, go to 53:20 in this video. Credit: Adapted from White House video.

Tackling Cancer Metastasis with Engineered Blood Platelets

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Tara Deans
Credit: Dan Hixson/University of Utah College of Engineering, Salt Lake City

When cancer cells spread to new parts of the body in a process called metastasis, they often get there by traveling through the bloodstream. To avoid alerting the immune system and possibly triggering their demise, cancer cells coax circulating blood platelets to glom onto their surfaces and mask them from detection. This deceptive arrangement has raised a tantalizing possibility: What if blood platelets could be programmed to recognize and take out those metastasizing cancer cells?

Tara Deans, University of Utah, Salt Lake City, was recently awarded a 2019 NIH Director’s New Innovator Award to do exactly that. It’s an exciting opportunity for a researcher who stumbled onto this innovative strategy quite by accident.

Deans is a bioengineer and expert in designing synthetic gene circuits. These circuits consist of small collections of genetic “parts” that can be assembled and integrated to program cells to behave differently than their natural counterparts [1]. In her initial work, Deans got these specialized gene circuits to prompt blood-forming stem cells to mass-produce platelets in the lab.

But blood platelets are unusual cells. They’re packed with many proteins that help to repair small nicks in blood vessels and stop the bleeding when we’re injured. Blood platelets do so even though they lack a nucleus and DNA to encode and make any of the proteins. Their protein cargo is pre-packaged and comes strictly from the bone marrow cells, called megakaryocytes, that produce them.

Deans realized that engineering platelets might pose a rare opportunity. She could wire the needed circuitry into the blood-forming stem cells and engineer them to make any desired therapeutic proteins, which are then loaded into the blood platelets for their 8- to 10-day lifespan. She started out producing blood platelets that could safely carry functional replacement enzymes in people with certain rare metabolic disorders.

As this research progressed, Deans got some troubling personal news: A friend was diagnosed with a blood cancer. At the time, Deans didn’t know much about the diagnosis. But, in reading about her friend’s cancer, she learned how metastasizing tumor cells interact with platelets.

That’s when Deans had her “aha” moment: maybe the engineered platelets could also be put to work in preventing metastasizing tumor cells from spreading.

Now, with her New Innovator Award, Deans will pursue this novel approach by engineering platelets to carry potentially promising cancer-fighting proteins. In principle, they could be tailored to fight breast, lung, and various other cancer types. Ultimately, she hopes that platelets could be engineered to target and kill circulating cancer cells before they move into other tissues.

There’s plenty of research ahead to work out the details of targeting the circulating cancer cells and then testing them in animal models before this strategy could ever be attempted in people. But Deans is excited about the path forward, and thinks that platelets hold great promise to function as unique drug delivery devices. It has not escaped her notice that this approach could work not only for controlling the spread of cancer cells, but also in treating other medical conditions.


[1] Genetic circuits to engineer tissues with alternative functions. Healy CP, Deans TL. J Biol Eng. 2019 May 3;13:39.


Metastatic Cancer (National Cancer Institute/NIH)

Deans Lab (University of Utah, Salt Lake City)

Deans Project Information (NIH RePORTER)

NIH Director’s New Innovator Award (Common Fund)

NIH Support: Common Fund; National Cancer Institute

Insurance Status Helps Explain Racial Disparities in Cancer Diagnosis

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Diverse human hands
Credit: iStock/jmangostock

Women have the best odds of surviving breast cancer if their disease is caught at an early stage, when treatments are most likely to succeed. Major strides have been made in the early detection of breast cancer in recent years. But not all populations have benefited equally, with racial and ethnic minorities still more likely to be diagnosed with later-stage breast cancer than non-Hispanic whites. Given that recent observance of Martin Luther King Day, I thought that it would be particularly appropriate to address a leading example of health disparities.

A new NIH-funded study of more than 175,000 U.S. women diagnosed with breast cancer from 2010-2016 has found that nearly half of the troubling disparity in breast cancer detection can be traced to lack of adequate health insurance. The findings suggest that improving insurance coverage may help to increase early detection and thereby reduce the disproportionate number of breast cancer deaths among minority women.

Naomi Ko, Boston University School of Medicine, has had a long interest in understanding the cancer disparities she witnesses first-hand in her work as a medical oncologist. For the study published in JAMA Oncology, she teamed up with epidemiologist Gregory Calip, University of Illinois Cancer Center, Chicago [1]. Their goal was to get beyond documenting disparities in breast cancer and take advantage of available data to begin to get at why such disparities exist and what to do about them.

Disparities in breast cancer outcomes surely stem from a complicated mix of factors, including socioeconomic factors, culture, diet, stress, environment, and biology. Ko and Calip focused their attention on insurance, thinking of it as a factor that society can collectively modify.

Many earlier studies had shown a link between insurance and cancer outcomes [2]. It also stood to reason that broad differences among racial and ethnic minorities in their access to adequate insurance might drive some of the observed cancer disparities. But, Ko and Calip asked, just how big a factor was it?

To find out, they looked to the NIH’s Surveillance Epidemiology, and End Results (SEER) Program, run by the National Cancer Institute. The SEER Program is an authoritative source of information on cancer incidence and survival in the United States.

The researchers focused their attention on 177,075 women of various races and ethnicities, ages 40 to 64. All had been diagnosed with invasive stage I to III breast cancer between 2010 and 2016.

The researchers found that a higher proportion of women receiving Medicaid or who were uninsured received a diagnosis of advanced stage III breast cancer compared with women with health insurance. Black, American Indian, Alaskan Native, and Hispanic women also had higher odds of receiving a late-stage diagnosis.

Overall, their sophisticated statistical analyses traced up to 47 percent of the racial/ethnic differences in the risk of locally advanced disease to differences in health insurance. Such late-stage diagnoses and the more extensive treatment regimens that go with them are clearly devastating for women with breast cancer and their families. But, the researchers note, they’re also costly for society, due to lost productivity and escalating treatment costs by stage of breast cancer.

These researchers surely aren’t alone in recognizing the benefit of early detection. Last week, an independent panel convened by NIH called for enhanced research to assess and explore how to reduce health disparities that lead to unequal access to health care and clinical services that help prevent disease.


[1] Association of Insurance Status and Racial Disparities With the Detection of Early-Stage Breast Cancer. Ko NY, Hong S, Winn RA, Calip GS. JAMA Oncol. 2020 Jan 9.

[2] The relation between health insurance coverage and clinical outcomes among women with breast cancer. Ayanian JZ, Kohler BA, Abe T, Epstein AM. N Engl J Med. 1993 Jul 29;329(5):326-31.

[3] Cancer Stat Facts: Female Breast Cancer. National Cancer Institute Surveillance, Epidemiology, and End Results Program.


Cancer Disparities (National Cancer Institute/NIH)

Breast Cancer (National Cancer Institute/NIH)

Naomi Ko (Boston University)

Gregory Calip (University of Illinois Cancer Center, Chicago)

NIH Support: National Center for Advancing Translational Sciences; National Cancer Institute; National Institute on Minority Health and Health Disparities

Giving Thanks for Biomedical Research

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This Thanksgiving, Americans have an abundance of reasons to be grateful—loving family and good food often come to mind. Here’s one more to add to the list: exciting progress in biomedical research. To check out some of that progress, I encourage you to watch this short video, produced by NIH’s National Institute of Biomedical Imaging and Engineering (NIBIB), that showcases a few cool gadgets and devices now under development.

Among the technological innovations is a wearable ultrasound patch for monitoring blood pressure [1]. The patch was developed by a research team led by Sheng Xu and Chonghe Wang, University of California San Diego, La Jolla. When this small patch is worn on the neck, it measures blood pressure in the central arteries and veins by emitting continuous ultrasound waves.

Other great technologies featured in the video include:

Laser-Powered Glucose Meter. Peter So and Jeon Woong Kang, researchers at Massachusetts Institute of Technology (MIT), Cambridge, and their collaborators at MIT and University of Missouri, Columbia have developed a laser-powered device that measures glucose through the skin [2]. They report that this device potentially could provide accurate, continuous glucose monitoring for people with diabetes without the painful finger pricks.

15-Second Breast Scanner. Lihong Wang, a researcher at California Institute of Technology, Pasadena, and colleagues have combined laser light and sound waves to create a rapid, noninvasive, painless breast scan. It can be performed while a woman rests comfortably on a table without the radiation or compression of a standard mammogram [3].

White Blood Cell Counter. Carlos Castro-Gonzalez, then a postdoc at Massachusetts Institute of Technology, Cambridge, and colleagues developed a portable, non-invasive home monitor to count white blood cells as they pass through capillaries inside a finger [4]. The test, which takes about 1 minute, can be carried out at home, and will help those undergoing chemotherapy to determine whether their white cell count has dropped too low for the next dose, avoiding risk for treatment-compromising infections.

Neural-Enabled Prosthetic Hand (NEPH). Ranu Jung, a researcher at Florida International University, Miami, and colleagues have developed a prosthetic hand that restores a sense of touch, grip, and finger control for amputees [5]. NEPH is a fully implantable, wirelessly controlled system that directly stimulates nerves. More than two years ago, the FDA approved a first-in-human trial of the NEPH system.

If you want to check out more taxpayer-supported innovations, take a look at NIBIB’s two previous videos from 2013 and 2018 As always, let me offer thanks to you from the NIH family—and from all Americans who care about the future of their health—for your continued support. Happy Thanksgiving!


[1] Monitoring of the central blood pressure waveform via a conformal ultrasonic device. Wang C, Li X, Hu H, Zhang, L, Huang Z, Lin M, Zhang Z, Yun Z, Huang B, Gong H, Bhaskaran S, Gu Y, Makihata M, Guo Y, Lei Y, Chen Y, Wang C, Li Y, Zhang T, Chen Z, Pisano AP, Zhang L, Zhou Q, Xu S. Nature Biomedical Engineering. September 2018, 687-695.

[2] Evaluation of accuracy dependence of Raman spectroscopic models on the ratio of calibration and validation points for non-invasive glucose sensing. Singh SP, Mukherjee S, Galindo LH, So PTC, Dasari RR, Khan UZ, Kannan R, Upendran A, Kang JW. Anal Bioanal Chem. 2018 Oct;410(25):6469-6475.

[3] Single-breath-hold photoacoustic computed tomography of the breast. Lin L, Hu P, Shi J, Appleton CM, Maslov K, Li L, Zhang R, Wang LV. Nat Commun. 2018 Jun 15;9(1):2352.

[4] Non-invasive detection of severe neutropenia in chemotherapy patients by optical imaging of nailfold microcirculation. Bourquard A, Pablo-Trinidad A, Butterworth I, Sánchez-Ferro Á, Cerrato C, Humala K, Fabra Urdiola M, Del Rio C, Valles B, Tucker-Schwartz JM, Lee ES, Vakoc BJ9, Padera TP, Ledesma-Carbayo MJ, Chen YB, Hochberg EP, Gray ML, Castro-González C. Sci Rep. 2018 Mar 28;8(1):5301.

[5] Enhancing Sensorimotor Integration Using a Neural Enabled Prosthetic Hand System


Sheng Xu Lab (University of California San Diego, La Jolla)

So Lab (Massachusetts Institute of Technology, Cambridge)

Lihong Wang (California Institute of Technology, Pasadena)

Video: Lihong Wang: Better Cancer Screenings

Carlos Castro-Gonzalez (Madrid-MIT M + Visión Consortium, Cambridge, MA)

Video: Carlos Castro-Gonzalez (YouTube)

Ranu Jung (Florida International University, Miami)

Video: New Prosthetic System Restores Sense of Touch (Florida International)

NIH Support: National Institute of Biomedical Imaging and Bioengineering; National Institute of Neurological Diseases and Stroke; National Heart, Lung, and Blood Institute; National Cancer Institute; Common Fund

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