In an interview with Targeted Oncology, Florencia McAllister, MD, discussed the data from these analyses of the tumor microbiome in patients with pancreatic cancer and their potential significance. She also discussed the next steps necessary for validating these results.
Florencia McAllister, MD
A recent analysis, led by investigators at The University of Texas MD Anderson Cancer Center, demonstrated that long-term survivors of pancreatic cancer have different microbiome signatures in their tumor microenvironments that impact the immune system compared with patients categorized as short-term survivors. Research showed that the bacteria can either stimulate or suppress immune response in patients with pancreatic cancer.
When the investigators conducted a mouse model study of fecal microbiota transplants (FMT) from patients, they found that the mice with FMT from long-term survivors had smaller tumors compared with the short-term survivors or control donors due to the composition of the tumor microbiome.
Next, the researchers looked at bacteria in tumors of both long-term and short-term survivors of pancreatic cancer. Data for 2 cohorts were collected, one at MD Anderson, which made up the discovery cohort, and a validation cohort at John Hopkins Hospital. The median survival was 10 years in long-term survivors and 1.6 years in short-term survivors at MD Anderson. In the cohort from John Hopkins, the long-term survivors had an overall survival greater than 10 years versus less than 5 years in the short-term survivors.
Long-term survivors had a greater diversity of bacterial specimen in the tumor microbiome than the short-term survivors, according to analysis using 16S ribosomal RNA gene sequencing. The diversity impact on survival was independent of other factors including treatments, body mass index, and antibiotics use. Researchers concluded these bacteria can be used as a predictor of survival and identified an intratumoral microbiome signature, making it an important potential biomarker.
Researchers then transplanted fecal microbiota from patients with pancreatic cancer into mice. Analysis showed that the transplanted microbiome represented 5% of the tumor microbiome and 70% had been altered by the transplant, demonstrating that the tumor microbiome can be altered.
After inducing stool transplants into the mice, researchers found that the FMT from long-term survivors significantly increased CD8-positive T-cell count and caused a greater activation of the CD8-positive T cells. Mice that received FMT from short-term survivors had an increase in immunosuppressive regulatory T cells and myeloid-derived suppressor cells, suggesting the potential to reverse immune suppression and affect tumor growth.
In an interview withTargeted Oncology, Florencia McAllister, MD, lead investigator and assistant professor of clinical cancer prevention at MD Anderson, discussed the data from these analyses of the tumor microbiome in patients with pancreatic cancer and their potential significance. She also discussed the next steps necessary for validating these results.
TARGETED ONCOLOGY: What was the rationale for conducting this study?
McAllister:We know that a few patients have good outcomes after surgery, but only very few patients. We wondered what the results for that were. Two years ago, there was a [study] that looked at the genetic differences in those patients. They actually did not find differences in those patients who do super well, called ‘long-term survivors’ [compared with short-term survivors]. They actually looked at the patients surviving more than 10 years, so we thought if there were no genetic differences, let’s look at non-genetic factors that could explain the long-term survivorship.
We did look at the immune microenvironment. Another study had looked at these long-term survivors a few years ago, and they did find more immune infiltration on the tumors for long-term survivors. They also found some stronger neoantigens, and they found that they were potentially responding to microbes. We again looked at the immune profile and directly looked at the microbe expression on the tumor; we found that there were differences in the microbiome’s composition in the tumor in the long-term survivors compared with the short-term survivors in both cohorts that we looked at.
TARGETED ONCOLOGY: What were the methods of design for this trial?
McAllister:We basically did this study with 2 sites, MD Anderson Cancer Center and John Hopkins Hospital, mainly because we thought we needed 2 geographically different cohorts since the tumor microbiomes can be affected by geographic regions, diets, etc. In each site, we first looked at the long-term survivors. MD Anderson is where we did the precise case-control. We first found the long-term survivors and then with that, [we defined] the controls that were matched for age, sex, stage of disease, diagnosis, treatment, and others. The second cohort, which is more of a validating cohort, we were only provided with the case-control, long-term survivors and short-term survivors. We didn’t do precise matching as much as at our institution because we didn’t have much of the clinical information.
We used tissue collection and tissue extraction for 16S rRNA gene sequencing, and at the same time we also did immune profiling of the same patients. It took us a long time to do. It’s a process to get the tissue with reliable data and have a bioinformatics pipeline that will actually process that information to give us meaningful data.
TARGETED ONCOLOGY: What were the findings?
McAllister:We found higher diversity in the long-term survivors from both cohorts, meaning more heterogeneity of bacteria. We also found that the long-term survivors [appeared] differentiated from the short-term survivors using the data from microbiome data analysis, suggesting potential differences in the specific bacteria from each group.
The next thing we did was look at specific compositions of the microbiome in both the short-term and long-term survivors. We found specific bacteria that were enriched in the long-term survivors were absent in most of the short-term survivors. This signature combined with the use of biomarkers could predict survivorship.
We also looked at immune profiling of the tumors, and response and immune activation as previously reported in the long-term survivors. Interestingly, we found a correlation between the immune activation and the presence of 3 bacteria found in the long-term survivors.
The next thing we wanted to do is find out if there could be potential control [achieved by] modulating the tumor microbiome to affect outcomes. Since the pancreas is a difficult-to-access organ, ideally we wanted to modulate the tumor microbiome. We thought that if there is some type of crossover on the tumor, we could ultimately change the tumor.
For that, we designed a small study in which we collected stools from patients that were going for Whipple surgery and also collected tumor and adjacent normal tissue. We collected those 3 specimens from patients going to surgery, and then we compared the microbiome composition in each patient in the experiment. It was very interesting to us that around 20% to 25% of the bacteria found on the tumors were actually found in the gut microbiome, whereas the normal adjacent tissue did not have this type of bacteria, suggesting that there is an initial translocation of the bacteria from the gut to the tumor. [This suggests that] you could modulate the gut microbiome to alter the tumor microbiome.
Based on that, we went ahead and collected a larger amount of fecal specimen from patients with pancreatic cancer that have survived the disease who have no evidence of disease now and from healthy controls. Those specimens were injected into mice and pretreated with antibiotics, and we then challenged them with tumors. Our main question was, can we actually modulate the tumor microbiome and the tumor immune profile to [affect] tumor growth? Indeed, we found that when you do that, you can change the tumor microbiome, and these result in changes in tumor growth and in the tumor immune profile, where the mice that received the stool from the patients with pancreatic cancer have bigger tumors and more immune-suppressive microenvironments than those that who received stool from long-term survivors or healthy controls; these mice had smaller tumors and a more immune-optimized profile.
Finally, what we did with this group was we looked at CD8 because we wanted to ask the question if modulation of the immune system could actually impair that effect. We found that indeed if you block CD8, the mice with tumors from long-term survivors now lose that antitumor effect, suggesting that there may be some bacteria status for the active immune system and the effect is ultimately mediated by the T cells.
TARGETED ONCOLOGY: What are the next steps planned for this research?
McAllister:We want to understand how the bacteria gets to the tumor and if we can modulate that. We also would like to be able to combine these bacteria and understand if it has a direct role on modulating immune suppression, inducing more immune optimization, like if it can ultimately affect tumor growth. We would also like to understand the role of modulation of the captive tumor, like relapses, to improve responses to other therapies that already exist like chemotherapy or immunotherapy that have limited efficacy in this patient population.
TARGETED ONCOLOGY: What is the main take-home message?
McAllister:We have found a microbiome signature that has to be validated but could potentially predict survivorship. We also have found that there is a crosstalk between the gut and the tumor microbes; therefore, we could potentially alter the tumor microbiomes by altering the gut microbiome. We also found that modulation of gut-to-tumor microbiome could result in reversing the immune suppression of pancreatic cancer and ultimately affect tumor growth.
TARGETED ONCOLOGY: What else is important to note about this research?
McAllister:We definitely want to proceed with a small proof-of-concept trial in which we can test if we can actually make a difference in the tumor microenvironment in patients with pancreatic cancer. Can we make a difference in the tumor microbiome by normalizing the bacteria found in pancreatic cancer development?
Riquelme E, Zhang Y, Zhang L, et al. Tumor microbiome diversity and composition influence pancreatic cancer outcomes.Cell.2019;178(4):795-806.e12. doi: 10.1016/j.cell.2019.07.008.