Broad Institute, MGH researchers chart cellular complexity of brain tumors

Pathology2Scientists from the Broad Institute and Massachusetts General Hospital (MGH) have conducted a first-of-its-kind study that characterizes the cellular diversity within glioblastoma tumors from patients. The study, which looked at the expression of thousands of genes in individual cells from patient tumors, revealed that the cellular makeup of each tumor is more heterogeneous than previously suspected. The findings, which appear online in Science Express, will help guide future investigations into potential treatments for this devastating disease.

This is the first time a large-scale census of the individual cells residing in these brain tumors has been taken. Researchers were previously aware that the cells within a human tumor were not all the same – they could have different mutations in their genome and possibly express genes differently – and it is suspected that this diversity may contribute to drug resistance and disease recurrence. But until now, it had been difficult to quantify the extent of this diversity.

To chart such differences, the researchers used a relatively new approach called single-cell transcriptomics, which allowed them to look at gene expression patterns in each of 430 individual cells from five patients’ brain tumors. These patterns, which vary from cell to cell, show which genes are switched on and which are switched off in a given cell, revealing information about the cell’s nature and function.

Previous studies of glioblastoma looked at the average expression of genes across millions of cells, which were slurried together in a single sample. In some cases, this type of sampling is used to classify glioblastoma tumors into one of four recognized cancer sub-types, based on the gene expression program that is most prevalent. By examining the gene expression patterns of many individual cells, one at a time, the team was able to get a finer picture of the cellular composition of the tumors. Their study revealed that each glioblastoma tumor contains individual cells from multiple cancer sub-types, and that the distribution of these cells varies from tumor to tumor.

The study also found that the cancer cells in these tumors exist in many states. Some are stem-cell-like, suggesting they have the capacity to self-renew and may play a role in tumor regeneration even after therapy. Others are the more mature, differentiated cancer cells that make up the bulk of the tumor. But the researchers also found that many cells exist on a spectrum between these states. Existing treatments, which only target the most prevalent cells in the tumor, may miss some of these sub-populations.

“To focus on the aspects of heterogeneity that we thought could be clinically relevant, we looked primarily for distinct cell states, and found multiple sub-populations in each tumor. Clinically, what this means is that we might need to treat each tumor based on the complement of cellular sub-types it contains – not just the most prevalent one,” said co-senior author Aviv Regev. Regev is a Broad Institute core member and director of the Broad’s Klarman Cell Observatory, as well as an associate professor at MIT and an Early Career Scientist with the Howard Hughes Medical Institute.

The researchers hope that these findings will help guide future investigations and approaches to treatment for glioblastoma, which is the most common and most aggressive form of brain cancer in adults.

“This is an incurable disease. There are existing therapies that may target 99 percent of the cells, but the tumors always come back. Understanding the cellular landscape can provide a blueprint for identifying new therapies that target each of the various sub-populations of cancer cells, and ultimately for tailoring such therapies to individual patient tumors,” said co-senior author Bradley Bernstein. Bernstein is a senior associate member of the Broad and professor of pathology at Massachusetts General Hospital and Harvard Medical School. He is also an Early Career Scientist of the Howard Hughes Medical Institute and a principal investigator at the Broad’s Klarman Cell Observatory.

In addition to Bernstein and Regev, the study was led by co-first authors Anoop Patel and Itay Tirosh, who are postdoctoral fellows in the Bernstein and Regev labs respectively, and co-senior author Mario Suvà, an assistant professor of pathology at MGH and a Broad associated scientist. The team represented a path-forging partnership between physicians and researchers from MGH’s Departments of Neurosurgery and Pathology, and molecular and computational biologists at the Broad. The collaboration brought together neurosurgeons and pathologists at MGH, led by Patel and Suvà, who removed the tumors from patients and molecularly characterized the samples; Broad biologists, led by John Trombetta and Alex Shalek, who conducted the single-cell analysis; and a computational team, led by Tirosh, that analyzed the data.

The team anticipates that the method and collaborative model will be effective in characterizing other cancer tumor types. Efforts to study additional cancers using the same methodology are currently underway.

The study was funded by the Klarman Family Foundation, as well as the National Institutes of Health, Howard Hughes Medical Institute, the Burroughs Wellcome Fund, and the Harvard Stem Cell Institute.

Other researchers who worked on the study include Shawn Gillespie, Hiraoki Wakimoto, Daniel Cahill, Brian Nahed, William Curry, Robert Martuza, David Louis, and Orit Rozenblatt-Rosen.

Paper cited:

Patel, AP et al. “Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.Science Express. Online June 12, 2014. DOI: 10.1126/science.1254257
About the Broad Institute of MIT and Harvard
The Eli and Edythe L. Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods and data openly to the entire scientific community.

Founded by MIT, Harvard and its affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to

Tiny, Simple-to-Use Lensless Microscope Might Soon Find a Place in Pathology

Pathology_June 26Imagine pathologists working with microscopes that don’t have a lens! That may be the future if technology currently under development by a UCLA engineering team can be used in various anatomic pathology or clinical laboratory applications.

UCLA engineer Aydogan Ozcan, Ph.D., introduced his newest invention, a novel lensless microscope, in the journal, Lab on a Chip. The world’s smallest, lightest microscope is about the size of a large egg and built on the LUCAS (Lensless Ultra-wide-field Cell Monitoring Array) platform previously invented by Ozcan for use in telemedicine.

Instead of magnifying samples, LUCAS generates holographic images of micro-particles or cells. A light-emitting diode illuminates the objects, and a digital sensor array captures their images.

This powerful lensless imaging system uses an optoelectronic sensor chip to detect the classical diffraction pattern, or shadow, of micro-particles in a sample. The acquired shadow image is digitally processed using a custom-developed decision algorithm to identify the particle location in 3D and characterize each micro-particle type within the sample. Different cell types (such as red blood cells and fibroblasts) or other micro-particles exhibit uniquely different shadow patterns and, therefore, can be rapidly identified without any ambiguity.

“This is a very capable and yet cost-effective microscope, shrunk into a very small package,” stated Ozcan. “Our goal with this project was to develop a device that can be used to improve health outcomes in resource-limited settings.”

The microscope is a self-contained imaging device that only requires a USB connection to a smart-phone, PDA, or computer to supply it with power and upload images. The computer analyzes the images and produces results instantly. For certain types of diagnostic procedures in resource-limited countries or environments, this technology could eliminate the need for skilled laboratory technicians.

Samples are loaded using a small chip filled with saliva or a blood smear. The lensless microscope is capable of identifying cells and particles in blood smears, including red blood cells, white blood cells and platelets.

Ozcan and his team developed this technology with an expectation that it could transform global healthcare in remote regions of the world. The technology is simple to use and durable. This makes it ideal for monitoring diseases like malaria, HIV, and tuberculosis in places that lack healthcare facilities. Samples do not have to be scanned or perfectly aligned in the microscope. Instead, the chip simply needs to be filled with a sample, then slid into a slot on the side of the microscope. Additionally, there are few moving parts, and the large aperture is resistant to problems caused by debris that might clog the light source of Ozcan’s lensless microscope.

The LUCAS microscope also can be used to field test water quality following a hurricane, earthquake or other disaster. It can be easily converted into a differential interference contrast (DIC) microscope, also known as a Nomarski microscope, by adding a few parts that cost about $1 to $2. DIC microscopes are used to gain information on the density of a sample, giving the appearance of a 3-D image by putting lines and edges in stark contrast.

The major effort is to find applications for the lensless microscope in resource-limited settings. For example, integrated telemedicine networks that employ tools like the lensless microscope will be essential to filling gaps in physical infrastructure by connecting mobile health-care providers to a central clinical pathology laboratory or hospital.

Pathologists and clinical laboratory managers may thus see the first applications of the lensless microscope as part of telemedicine initiatives that support healthcare in more remote or underdeveloped regions.

–K. Branz

Related Information:

UCLA engineer invents world’s smallest, lightest telemedicine microscope

Compact, light-weight and cost-effective microscope based on lensless incoherent holography for telemedicine applications

UCLA engineer makes lensless microscope even tinier for resource-limited settings

Read more: Optoelectronic Sensor Chip: Tiny Simple-to-Use Lensless Microscope Might Soon Find a Place in Pathology | Dark Daily

Icahn School of Medicine at Mount Sinai

LogoIcahn School of Medicine at Mount Sinai is proud to stand as a leader in medical and scientific training, biomedical research and patient care. Our unwavering dedication to intellectual exchange, multidisciplinary teamwork and innovation propels us ever forward in discoveries and advances to improve the human condition.

Icahn School of Medicine attracts outstanding scientists, clinicians and students, all of whom share a deep commitment to expanding biomedical knowledge, providing expert clinical care and serving the community. Working in close partnership with The Mount Sinai Hospital, the Icahn School of Medicine serves one of the most diverse and complex patient populations in the world. Our passion for patient-focused research and education has inspired generations of physicians and researchers to learn, teach and practice breakthrough translational medicine on our campus. Fast paced and forward thinking, we continue to build upon this legacy.

My Video

My Entry into the Leading Physicians of the World

LPW - smallHey everyone! Check out my official entry into the Leading Physicians of the World:

Carlos Cordon-Cardo, MD, PhD, Represents New York with Inclusion into Renowned Publication The Leading Physicians of the World