Durable response to anti-PD-1 immunotherapy in epithelioid ...
PRECISION TOOLS...By 2015, checkpoint inhibitors such as PD-1 blockers and PD-L1 blockers had taken...
Transcript of PRECISION TOOLS...By 2015, checkpoint inhibitors such as PD-1 blockers and PD-L1 blockers had taken...
PRECISION TOOLS
Unraveling the Microbiome’s Complex Role in Immunotherapy
by Randi Lundberg, DVM, Ph.D.
growing body of evidence has shown that the microbiome influences both the development of disease and patient response to therapy. In the field of immuno- oncology, new insights are coming to the forefront regarding the microbiome’s effect on tumor growth and targeted therapeutics, including immunotherapies such as checkpoint inhibitors. Research has progressed from demonstrating a link between the microbiome and cancer therapy in mice, to supporting those findings in human patients, to opening new possibilities to explore modulation of the microbiome as a personalized medicine strategy for improving immunotherapy efficacy.
Establishing a Link
Some of the first studies to demonstrate a
connection between the microbiome and
response to cancer treatment in mice were
published in 2013. Iida et al. looked at how
the microbiome impacted the efficacy of an
immunotherapy and a platinum-based
chemotherapy in tumor-bearing mice
lacking microbiota. Treatment efficacy was
reduced in germ-free mice and those treated
with antibiotics, suggesting that the gut
microbiome was important for activating an
anti-tumor immune response in the local
tumor microenvironment1. A different study
in the same publication found similar results,
with tumor-bearing mice that were germ-free
or administered antibiotics before treatment
with the oncology drug cyclophosphamide
having impaired anti-tumor response
Investigators began to consider whether
non-responder patients’ microbiomes were
impacting their anti-tumor response. Two
studies in mice arrived at the same overall
conclusion: The microbiome can modulate
response to checkpoint inhibitor therapy,
impacting its efficacy. These studies found
that certain microbiota appear beneficial to
treatment response and others detrimental,
while the use of antibiotics to modulate the
microbiome can impact anti-tumor response.
In studying melanoma progression in mice
with different microbiota, researchers at the
University of Chicago found variations in
spontaneous anti-tumor activity. The
presence of Bifidobacterium was associated with
anti-tumor activity, and administering it orally
resulted in the same level of tumor control
seen with PDL-1 therapy3.
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and drug resistance2. Together, these two
articles articulated the necessity of an intact
commensal gut microbiota to stimulate the
innate and adaptive immune system in a way
that the immune system is in better shape to
mount an anti-tumor response during therapy.
By 2015, checkpoint inhibitors such as PD-1
blockers and PD-L1 blockers had taken center
stage as a highly promising immunotherapy
approach, shifting the research focus to
exploring how the microbiome might impact
the efficacy of this groundbreaking therapy.
Checkpoint inhibitors, which work by
preventing cancer cells from switching off T
cells’ anti-cancer activity, have proven very
effective in some patients. Yet, for a subset of
the cancer patient population this treatment
approach has failed to work.
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Similarly, French researchers studied whether
the efficacy of Ipilimumab (Yervoy®) in
blocking CTLA-4 would be affected by the
composition of the microbiome in mice
bearing melanoma tumors. Both the germ-free
mice and those treated first with antibiotics
did not respond to the CTLA-4 checkpoint
blockade, while the treatment was more
efficacious in mice and patients carrying
bacteria species such as Bacteroides
thetaiotaomicron and B. fragilis4.
From Mice to Men
More recently, three studies in humans have
supported these findings in mice. Published in
November 2017 and January 2018 in Science,
the studies focused on variations in the
microbiomes of patients who respond
well to checkpoint inhibitor therapy vs.
those who do not. The three studies
demonstrated similar results across institutions
in two countries, multiple tumor types and a
variety of patient cohorts. Overall, responders
to immunotherapy displayed different
compositional and functional features of
their gut microbiomes than non-responders,
and fecal microbiota transplantation (FMT)
from patients to germ-free mice identified a
causal relationship between the microbiome
and response to immunotherapy.
The focus for researchers at the Gustav Roussy
Cancer Campus in Villejuif, France was to
review data on patients with non-small cell
lung, kidney or bladder cancer who received
treatment with a PD-1 checkpoint inhibitor.
Those who had taken antibiotics before or
soon after the start of treatment responded
less effectively to anti-PD-1 therapy, with
shorter progression-free survival and overall
survival. When germ-free mice received
fecal microbiota transplants from responder
patients, the PD-1 blockers were more
efficacious, and more CXCR3+CD4+ T cells
were observed in the tumor microenvironment5.
Researchers at the University of Texas MD
Anderson Cancer Center studied the oral and
intestinal microbiota of melanoma patients
under treatment with a PD-1 blocker, observing
a correlation between effective response to
anti-PD-1 therapy and two microbiome factors:
the diversity and the composition of the gut
microbiome. Patients with low levels of
Faecalibacterium and high levels of Bacteroidales
had shorter progression-free survival, meaning
the length of time during and after therapy
that a patient lives until either worsening
of the disease or death. When mice were
given fecal transplants from responder or
non-responder patients, their response to
the anti-PD-1 therapy was similar to patients’
response, and those with microbiota from
responders displayed more CD8+ T cells in
the tumor microenvironment6.
The third recently published study, conducted
at the University of Chicago, involved patients
with metastatic melanoma who were under
treatment with PD-L1 blockers. Those who
responded better to the anti-PD-L1 therapy
had a greater abundance of eight specific
bacteria. When the researchers evaluated
the efficacy of anti-PD-L1 therapy on mice
receiving FMT from responders and non-
responders, they discovered that the PD-L1
blocker was only effective in mice receiving
FMT from responders, with five of the eight
bacterial strains associated with anti-PD-L1
in patients also found in the mice7.
What’s Next?
With a relationship established between
the microbiome and anti-tumor response,
the door now opens to exploring whether
deliberate manipulation of the microbiome
could be an effective personalized
medicine strategy for cancer patients
undergoing checkpoint inhibitor therapy
or other forms of immunotherapy.
While there is a good deal of consistency in
the research findings to date in many respects,
there remains uncertainty about which
microbiome compositions correlate best with
an immunotherapy response. There is still
more work to be done in determining which
individual bacterial agents or microbiota
compositions are most beneficial in stimulating
or enabling an effective response to
immunotherapy, and whether those
correlations vary by tumor type or immuno-
therapy type. Studying such a complex
question will prove challenging, as some
of the associated bacteria have overlapping
functionalities; they also interact with each
other and with the host’s organs, creating
greater complexity. Germ-free mice will prove
a useful tool for this endeavor, as they can
serve as a blank slate for evaluating different
strains of bacteria under different conditions.
Germ-free mice may have a role in the clinic as
well, particularly in facilitating a personalized
approach to selection of an immunotherapy
strategy. Much like FMT helped to identify a
causal relationship between the microbiome
and anti-tumor response, this technique can
be used to help make decisions on the most
efficacious therapy for a given patient. Until
valid biomarkers based on the patient’s
microbiome profile are available, a germ-free
mouse implanted with fecal matter from a
cancer patient can be used to study the efficacy
of a particular drug prior to the patient
beginning a course of treatment. Such an
approach can be personalized to an even
greater degree by combining xenografting
of patient-derived tumor tissue to immune
system-humanized mice with patient micro-
biota transplantation. This holistic approach
enables a very precise evaluation of the specific
tumor type’s response to therapy in a
humanized immune system model, taking
the patient’s microbiome profile into account.
Use of this methodology can aid in selecting
the most efficient treatment from those
currently available, as well as exploring
questions such as what might be added to
the patient’s microbiome to make the
immunotherapy treatment more effective, or
how the immunotherapy might be adjusted to
better correspond to the patient’s microbiome.
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Already, several academic and industrial
partner collaborators have announced their
plans to test various bacterial candidates in
combination with different checkpoint
inhibitor therapies in trials involving patients
with advanced metastatic melanoma or other
cancer types.
Practical Considerations
With multiple studies demonstrating a
connection between the microbiome and
immunotherapy response, it is essential to
consider the baseline microbiome of the
mouse models employed when designing
immunotherapy drug efficacy studies. To
minimize study variability that could arise
from the microbiome’s effect, several factors
should be considered and controlled where
feasible.
Ideally, mice should be sourced from the
same vendor and the same barrier or other
production location to minimize microbiome
variations. If certain features of the microbi-
ome are necessary to have in place to test
the hypothesis, e.g. the presence of certain
Bacteroides species or Faecalibacterium, these
organisms can be introduced to the mice.
This approach covers the addition of
the bacteria of interest to the baseline
microbiome, or germ-free mice can be
used to start from scratch with an entire
microbiome of interest by FMT. When FMT
studies are conducted, the recipient mouse
should be germ-free ideally; an alternative
approach is to deplete the mouse’s
microbiome with antibiotic cocktails prior
to transplantation, though this may be less
reliable since off-target effects of drug
cocktails can occur.
It is equally important to understand the
animals’ housing and diet. If individually
ventilated cages are used, for example, the
microbiome of mice in a single cage can drift
and eventually diverge from the rest of the
colony, and such differences can become more
pronounced over multiple generations. The
composition of rodent chow can vary across
lots or seasonally, and microbial content can
vary by source location and processing
methods. Sticking to the same diet batch in
studies or using purified diets instead, together
with sterilization processes, can help to
mitigate these variances. Exposure to
pathogens, commensal bacteria in the
environment or from staff, or treatment
by antibiotics also can affect the animals’
microbiome, as can stress related to
transportation, housing conditions, or
disease. Treating the drinking water with
chlorine or acids to reduce bacterial growth
has also been shown to alter the microbiota.
As research on the microbiome’s impact
on cancer therapy has evolved, the complex
role of our gut microbiota on the efficacy
of immunotherapy has come into greater
focus. While much work remains to be done,
especially to understand which bacterial
agents best correlate with an anti-tumor
response, the most recent findings open
exciting opportunities to modulate the
microbiome on an individualized basis
to improve immunotherapy efficacy and
patient outcomes.
Randi Lundberg, DVM, Ph.D, is a Field Applications
Scientist, Taconic Biosciences. Dr. Lundberg is a Doctor
of Veterinary Medicine and holds a Ph.D. in
microbiome and experimental animals from the
University of Copenhagen. In 2018, Dr. Lundberg
received the prize of honor “Industrial Researcher
of the Year” for combining scientific excellence
with applicable business solutions.
References
1. Iida, N. et al. Commensal Bacteria Control Cancer Response to Therapy by Modulating the Tumor Microenvironment. Science (80-. ). 342, 967–970 (2013).2.Viaud, S. et al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 342, 971–6 (2013).3.Sivan, A. et al. Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy. Science (80-. ). 350, 1084–1089 (2015).4.Vetizou, M. et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science (80-. ). 350, 1079–1084 (2015).5.Routy, B. et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Science eaan3706 (2017). 6.Gopalakrishnan, V. et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science eaan4236 (2017). 7.Matson, V. et al. The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients. Science 359, 104–108 (2018).