Scientists develop faster, smarter way to classify tumors using single-cell technology

Dr. Stephen Lin, CIRM Senior Science Officer

By Dr. Stephen Lin

Single-cell.  It is the new buzzword in biology.  Single-cell biology refers to the in-depth characterization of individual cells in an organ or similar microenvironment.  Every organ, like the brain or heart, is composed of thousands to millions of cells.  Single-cell biology breaks those organs down into their individual cell components to study the diversity within those cells.  For example, the heart is composed of cardiomyocytes, but within that bulk population of cardiomyocytes there are specialized cardiomyocytes for the different chambers of the heart and others that control beating, plus others not even known yet.  Single-cell studies characterize cell-to-cell variability in the body down to this level of detail to gain knowledge of tissues in a way that was not possible before.   

The majority of single-cell studies are based on next generation sequencing technologies of genetic material such as DNA or RNA.  The cost of sequencing each base of DNA or RNA has dropped precipitously since the first human genome was published in 2000, often compared to the trend seen with Moore’s Law in computing.  As a result it is now possible to sequence every gene that is expressed in an individual cell, called the transcriptome, for thousands and thousands of cells.   

The explosion of data coming from these technologies requires new approaches to study and analyze the information.  The scale of the genetic sequences that can be generated is so big that it is often not possible anymore for scientists to interpret the data manually as had been traditionally done.  To apply this exciting field to stem cell research and therapies, CIRM funded the Genomics Initiative which created the Centers of Excellence in Stem Cell Genomics (CESCG).  The goal of the CESCG is to create novel genomic information and create new bioinformatics tools (i.e. computer software) specifically for stem cell research, some of which was highlighted in past blogs.  Some of the earliest single-cell gene expression atlases of the human body were created under the CESCG. 

The latest study from CESCG investigators creates both new information and new tools for single-cell genomics.  In work funded by the Genomics Initiative, Stephen Quake and colleagues at Stanford University and the Chan-Zuckerberg Biohub studied tumor formation using single-cell approaches.  Drawing from one of the earliest published single-cell studies, the team had surveyed human brain transcriptome diversity that included samples from the brain cancer, glioblastoma. 

Recognizing that the data coming from these studies would eventually become too large and numerous to classify all of the cell types by hand, they created a new bioinformatics tool called Northstar to apply artificial intelligence to automatically classify cell types generated by single-cell studies.  The cell classifications generated by Northstar were similar to the original classifications created manually several years ago including the identification of specific cancerous cells. 

Some of the features that make Northstar a powerful bioinformatics tool for these studies are that the software is scalable for large numbers of cells, it performs the computations to classify cells very fast, and it requires relatively low computer processing power to go through literally millions of data points. 

The scalability of the tool was demonstrated on the Tabula Muris data collection, a single-cell compendium of 20 mouse organs with over 200,000 cells of data.  Finally, Northstar was used to classify the tumors from new single-cell data generated by the CESCG via samples of 11 patient pancreatic cancer patients obtained from Stanford Hospital.  Northstar correctly found the origins of cancerous cells from the specific diagnoses of pancreatic cancer that the patients had, for example cancerous cells in the endocrine cell lineage from a patient diagnosed with neuroendocrine pancreas cancer.  Furthermore, Northstar identified previously unknown origins of cancerous cell clusters from other patients with pancreatic cancer.  These new computational tools demonstrate how big data from genomic studies can become important contributors to personalized medicine.

The full study was published in Nature.

Stories that caught our eye: FDA grants orphan drug status to CIRM-funded therapy; stunning discovery upends ideas of cell formation; and how tadpoles grow new tails

Gut busting discovery

Intestinal stem cells: Photo courtesy Klaus Kaestner, Penn Institute for Regenerative Medicine

It’s not often you read the word “sensational” in a news release about stem cells. But this week researchers at the University of Copenhagen released findings that are overturning long-held ideas about the development of cells in our stomachs. So perhaps calling it “sensational” is not too big a stretch.

In the past it was believed that the development of immature cells in our stomachs, before a baby is born, was predetermined, that the cells had some kind of innate sense of what they were going to become and when. Turns out that’s not the case. The researchers say it’s the cells’ environment that determines what they will become and that all cells in the fetus’ gut have the potential to turn into stem cells.

In the “sensational” news release lead author, Kim Jensen, says this finding could help in the development of new therapies.

“We used to believe that a cell’s potential for becoming a stem cell was predetermined, but our new results show that all immature cells have the same probability for becoming stem cells in the fully developed organ. In principle, it is simply a matter of being in the right place at the right time. Here signals from the cells’ surroundings determine their fate. If we are able to identify the signals that are necessary for the immature cell to develop into a stem cell, it will be easier for us to manipulate cells in the wanted direction’.

The study is published in the journal Nature.                             

A tale of a tail

African clawed frog tadpole: Photo courtesy Gary Nafis

It’s long been known that some lizards and other mammals can regrow severed limbs, but it hasn’t been clear how. Now scientists at the University of Cambridge in the UK have figured out what’s going on.

Using single-cell genomics the scientists were able to track which genes are turned on and off at particular times, allowing them to watch what happens inside the tail of the African clawed frog tadpole as it regenerates the damaged limb.

They found that the response was orchestrated by a group of skin cells they called Regeneration-Organizing Cells, or ROCs. Can Aztekin, one of the lead authors of the study in the journal Science, says seeing how ROCs work could lead to new ideas on how to stimulate similar regeneration in other mammals.

“It’s an astonishing process to watch unfold. After tail amputation, ROCs migrate from the body to the wound and secrete a cocktail of growth factors that coordinate the response of tissue precursor cells. These cells then work together to regenerate a tail of the right size, pattern and cell composition.”

Orphan Drug Designation for CIRM-funded therapy

Poseida Therapeutics got some good news recently about their CIRM-funded therapy for multiple myeloma. The US Food and Drug Administration (FDA) granted them orphan drug designation.

Orphan drug designation is given to therapies targeting rare diseases or disorders that affect fewer than 200,000 people in the U.S. It means the company may be eligible for grant funding toward clinical trial costs, tax advantages, FDA user-fee benefits and seven years of market exclusivity in the United States following marketing approval by the FDA.

CIRM’s President and CEO, Dr. Maria Millan, says the company is using a gene-modified cell therapy approach to help people who are not responding to traditional approaches.

“Poseida’s technology is seeking to destroy these cancerous myeloma cells with an immunotherapy approach that uses the patient’s own engineered immune system T cells to seek and destroy the myeloma cells.”

Poseida’s CEO, Eric Ostertag, said the designation is an important milestone for the company therapy which “has demonstrated outstanding potency, with strikingly low rates of toxicity in our phase 1 clinical trial. In fact, the FDA has approved fully outpatient dosing in our Phase 2 trial starting in the second quarter of 2019.”