Blood biopsy offers new view of tumor evolution in multiple myeloma

In order to diagnose multiple myeloma, a cancer of bone marrow-derived plasma cells, a physician must perform a bone marrow biopsy, inserting a large needle into the patient’s bone (usually the hip) and extracting a 1-inch-long sliver of marrow for analysis. The procedure is painful and costly, and therefore only done at initial diagnosis and when patients relapse. Getting a close look at tumor cells before cancer develops, while patients are undergoing treatment (when drug resistance typically appears), or during remission is just not practical today.

“Because of the invasiveness, time, and effort, bone marrow biopsies are only done at a few time points,” said Jens Lohr, a researcher at the Broad Institute of MIT and Harvard and an oncologist and investigator at the Dana-Farber Cancer Institute. “To capture the missing windows of time that are so important in the disease, we’d ideally have a test that gives us rich information about the genomic and functional state of tumor cells from a simple blood draw, which is done frequently during cancer care.”

To explore the feasibility of a blood test that could one day replace a bone marrow biopsy, Lohr, Broad core member and Cancer Program director Todd Golub, and Noopur Raje of Massachusetts General Hospital (MGH) Cancer Center devised a method to analyze the genomic features of single circulating myeloma cells isolated from peripheral blood. Featured in the November 2 issue of Science Translational Medicine, the team’s approach produces genomic information on par with, and in some cases better than, data from bone marrow biopsy. Because it relies on a routine blood sample, the test can be used to provide information about tumor cells at virtually any given point in time, something not feasible with bone marrow biopsy.

In the study, the researchers first isolated single myeloma cells from the blood of 24 patients with active disease by staining cells for plasma cell markers and then enriching and manually isolating the cells under the microscope. The researchers were able to recover at least 12 cancer cells from each study participant. They then subjected those individual cells to DNA sequencing at 35 genomic sites known to be frequently mutated in multiple myeloma, and compared the results to the sequencing of single cells from the bone marrow and to the genotyping of bulk bone marrow tissue (the test currently used clinically).

The single-cell analyses performed at the Broad uncovered the same DNA mutations that were found using the existing bulk bone marrow test. In addition, the single-cell approach was able to generate data for samples that were deemed to have insufficient DNA for the bulk bone marrow test, demonstrating the power of its sensitivity.

Interestingly, in some patients the blood biopsy analysis uncovered more mutations in known oncogenes than were detected in the bone marrow, which could be due to the high sensitivity of the single-cell approach. It also suggests that circulating tumor cells could be a better representation of a multiple myeloma patient’s many tumor sites throughout the body than bone marrow cells taken from a single site, giving the blood biopsy approach more power to capture the heterogeneity of multiple myeloma.

One finding in particular illustrated the interesting, new cancer biology that can be explored with the method, even in patients with very few cancer cells in the blood. Among the patients in the study was one with a pre-cancerous disease known as monoclonal gammopathy of undetermined significance (MGUS). Only 1% of MGUS patients progress to multiple myeloma each year, and many of those patients may never develop full-blown cancer. For this reason, MGUS patients are normally not given a bone marrow biopsy until certain protein markers reach a threshold level in the blood, at which point they may have already progressed to cancer. The new analyses showed that this MGUS patient’s cells harbored a mutation in NRAS, a known oncogene. “It makes you wonder: Will this patient develop cancer soon? If he has an oncogene mutation but doesn’t develop cancer, why not?” asked Lohr. With an effective blood biopsy test for myeloma, MGUS patients could potentially be followed to track the development of their disease and to prevent or slow the progress of cancer early on.

While chemotherapy remains a first line treatment for multiple myeloma patients, drug resistance is a major problem. “Fifteen years ago, the average survival of these patients was two to three years, and with new therapies coming to market (several in 2015 alone), survival is going up and up,” said Lohr. “Today we have drugs that work well, yet we unfortunately are still looking for ways to cure patients. Everyone eventually develops drug resistance.”

The new work adds to the growing body of evidence illustrating the power of circulating tumor cell analysis, a field pioneered by Broad associate member Daniel Haber, also director of the MGH Cancer Center. Circulating tumor cells have the potential to give scientists an unprecedented window into the evolution of resistance in tumor cells during chemotherapy. Even those multiple myeloma patients who respond the best to chemotherapy will have “minimal residual disease” with a small number of cancer cells — potentially the most drug-resistant ones — still present in the body. Single-cell analysis of tumor cells from the blood offers an opportunity to isolate and study those resistant cells throughout the course of therapy, giving the oncologist critical information to help tailor chemotherapy to a patient’s evolving disease.

In addition to looking for genetic mutations, the team also performed RNA sequencing on the cells as a measure of cellular function. With the transcriptome data, they were able to distinguish myeloma cells from healthy plasma cells, and detect subpopulations of myeloma cells present in a sample. RNA sequencing also easily measured expression of genes that are targeted by therapeutic antibodies, suggesting that the method could be used to study how cells become resistant to drugs, such as through reduced expression of those target genes or mutation of a target protein’s binding site.

“In this study, we’ve shown that single-cell technologies can produce extremely high-resolution genomic information about circulating multiple myeloma cells in a large number of patients at many time points,” said senior author Golub, also director of the Broad’s Cancer Program and the Charles A. Dana Investigator in Human Cancer Genetics at the Dana-Farber Cancer Institute. “But there is still more work to be done before this approach can help the thousands of patients battling this disease.”

While a blood test for multiple myeloma is not yet ready to replace a bone marrow biopsy, the study of circulating tumor cells throughout the course of cancer could shed light on why multiple myeloma is so difficult to cure. “Even if they don’t become routine clinical markers, circulating tumor cells stand to become a terrific biological tool to shed light on the mystery of drug resistance in this incurable disease,” said Lohr.

Other Broad researchers involved in the work include Sora Kim, Joshua Gould, Birgit Knoechel, Yotam Drier, Matthew Cotton, Daniel Gray, Bang Wong, Gavin Ha, Cheng-Zhong Zhang, Guangwu Guo, Matthew Meyerson, and Jesse Boehm.