An atlas of an aggressive leukemia

February 28, 2019

February 28, 2019, NEW YORK-- A team of researchers led by Bradley Bernstein at the Ludwig Center at Harvard has used single-cell technologies and machine learning to create a detailed "atlas of cell states" for acute myeloid leukemia (AML) that could help improve treatment of the aggressive cancer.

AML is characterized by the accumulation of white blood cells in the bone marrow and blood. The disease is notoriously difficult to study because the bone marrow of AML patients contains a variety of normal and malignant cell types. This includes undifferentiated primitive cancer cells with stem cell-like properties and differentiated mature cancer cells that affect the tumor environment in different ways. AML cells also constantly acquire DNA mutations, branching into lineages of related "subclones."

"We've known in a qualitative way since the 1960s that AML tumors are heterogenous mixtures of cells," said Peter van Galen, a lead coauthor of the paper and a postdoctoral research fellow in Bernstein's lab at Massachusetts General Hospital. "Now, we have a very quantitative way of determining the different cell types present within these tumors."

In the new study, which will be published online on February 28 in the journal Cell, Bernstein and his colleagues, including Ludwig Harvard investigators Jon Aster and Andrew Lane, combined cutting-edge technologies--single-cell RNA (scRNA) sequencing, long-read nanopore DNA sequencing and machine learning--to distinguish normal cells from cancerous ones and organize them based on their DNA sequence and gene expression similarities.

"This project was an interdisciplinary effort that connected engineers at MIT and the Broad Institute to cancer researchers and oncologists at the Massachusetts General Hospital, Dana-Farber Cancer Institute and Brigham and Women's Hospital," said Bernstein, of the Ludwig Center at Harvard, Harvard Medical School and Massachusetts General Hospital.

"We couldn't have done this without the vision that the Ludwig directors had in funding an effort to begin banking leukemia samples," added Bernstein.

scRNA sequencing captures a snapshot of a cell's entire transcriptome--that is, all the mRNA molecules present in a cell at a given moment. This allows researchers to break down a population of cells into distinct types and to track the evolution of cellular lineages. The team employed a new scRNA sequencing method to capture the full transcriptomes of nearly 40,000 bone marrow cells gathered from 16 AML patients and five healthy donors.

"This is the first time this has been done in a high-throughput manner," said study co-first author Volker Hovestadt, a postdoctoral research fellow in Bernstein's lab. "Instead of profiling only a couple hundred single cells, we were able to profile tens of thousands."

But the gene expression profile of AML cells can resemble that of normal ones. To address this challenge, the team performed single-cell genotyping on the bone marrow cells, screening them for a set of known AML genetic markers to pick out those that were cancerous. "To really nail this, we had to incorporate a third-generation DNA sequencing technique called long-read nanopore sequencing, which enhanced detection of mutations across the genome," van Galen said.

Long-read sequencing scans much longer DNA fragments, boosting the odds of capturing all mutations accumulated in a gene. It allowed the researchers to more efficiently identify descendants of differently mutated cells, called subclones, that can variably affect the cancer's growth rate, metastatic potential and response to therapy.

Lastly, the researchers employed a machine learning algorithm to bring the scRNA sequencing and genotyping data together. The end result was a map or "atlas" of different AML cell types and the normal blood cell types with which they co-exist in the bone marrow environment.

The atlas allowed the researchers to see at a glance not only which cells were cancerous, but also their states--primitive, differentiated or in the process of differentiating. Since tumor samples were gathered from patients at different timepoints, the researchers could also compare the developmental hierarchies of AML tumors between individuals and track the evolution of those hierarchies from first diagnosis through treatment and outcome.

The researchers show that the transcriptional programs of AML cells are aberrantly regulated. "In normal cells, development progresses in stages. You go from cell type X to cell type Y," Bernstein said. "These leukemia cells co-express a mish-mash of genes from different stages."

The researchers also discovered multiple subclonal populations within a single AML patient. "In at least one case, the two subclones behaved completely differently and had different gene expression profiles," Bernstein said. "One subclone was mostly differentiating while the other was arrested in a highly aggressive state, and the aggressive subclone had a mutation that was consistent with a poor patient prognosis."

The findings may also explain why therapies that harness T cells of the immune system to target tumors have been relatively less successful against AML. The researchers identified a class of cells that behaved like white blood cells known to suppress anticancer immune responses.

"You might assume that these are normal cells, but when you look at their genotype, you see that they harbor leukemic mutations," Bernstein said. "These are cells that the tumor is producing to suppress the immune system. It's an adaptive survival mechanism for the tumor."

Their findings, the researchers note, should aid in the development of novel strategies for immunotherapy and precision medicine for the treatment of AML.
This research was supported by Ludwig Cancer Research, the US National Institutes of Health, the National Cancer Institute and the National Human Genome Research Institute.

About Ludwig Cancer Research

Ludwig Cancer Research is an international collaborative network of acclaimed scientists that has pioneered cancer research and landmark discovery for more than 40 years. Ludwig combines basic science with the ability to translate its discoveries and conduct clinical trials to accelerate the development of new cancer diagnostics and therapies. Since 1971, Ludwig has invested $2.7 billion in life-changing science through the not-for-profit Ludwig Institute for Cancer Research and the six U.S.-based Ludwig Centers. To learn more, visit

For further information, please contact Rachel Reinhardt, or +1-212-450-1582.

Ludwig Institute for Cancer Research

Related Cancer Articles from Brightsurf:

New blood cancer treatment works by selectively interfering with cancer cell signalling
University of Alberta scientists have identified the mechanism of action behind a new type of precision cancer drug for blood cancers that is set for human trials, according to research published in Nature Communications.

UCI researchers uncover cancer cell vulnerabilities; may lead to better cancer therapies
A new University of California, Irvine-led study reveals a protein responsible for genetic changes resulting in a variety of cancers, may also be the key to more effective, targeted cancer therapy.

Breast cancer treatment costs highest among young women with metastic cancer
In a fight for their lives, young women, age 18-44, spend double the amount of older women to survive metastatic breast cancer, according to a large statewide study by the University of North Carolina at Chapel Hill.

Cancer mortality continues steady decline, driven by progress against lung cancer
The cancer death rate declined by 29% from 1991 to 2017, including a 2.2% drop from 2016 to 2017, the largest single-year drop in cancer mortality ever reported.

Stress in cervical cancer patients associated with higher risk of cancer-specific mortality
Psychological stress was associated with a higher risk of cancer-specific mortality in women diagnosed with cervical cancer.

Cancer-sniffing dogs 97% accurate in identifying lung cancer, according to study in JAOA
The next step will be to further fractionate the samples based on chemical and physical properties, presenting them back to the dogs until the specific biomarkers for each cancer are identified.

Moffitt Cancer Center researchers identify one way T cell function may fail in cancer
Moffitt Cancer Center researchers have discovered a mechanism by which one type of immune cell, CD8+ T cells, can become dysfunctional, impeding its ability to seek and kill cancer cells.

More cancer survivors, fewer cancer specialists point to challenge in meeting care needs
An aging population, a growing number of cancer survivors, and a projected shortage of cancer care providers will result in a challenge in delivering the care for cancer survivors in the United States if systemic changes are not made.

New cancer vaccine platform a potential tool for efficacious targeted cancer therapy
Researchers at the University of Helsinki have discovered a solution in the form of a cancer vaccine platform for improving the efficacy of oncolytic viruses used in cancer treatment.

American Cancer Society outlines blueprint for cancer control in the 21st century
The American Cancer Society is outlining its vision for cancer control in the decades ahead in a series of articles that forms the basis of a national cancer control plan.

Read More: Cancer News and Cancer Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to