Dr. Pierce and her team are working to develop protocols in the field of cancer epidemiology and microbiome research to better our understanding of the microbiome's role in patient response to cancer treatment. The long-term goal of our research is to identify microbial biomarkers that can predict patient response to treatment, information that could better aid a clinician in recommending certain therapies over others to their patients.
The Microbiome in Human Health
The human microbiome encompasses the totality of the genetic sequences of every microbe (including bacteria, viruses, and fungi) that lives within and on our bodies. The microbiota refers to the collection of microbial organisms (defined by taxonomy) that live within and on our bodies. These microbes have evolved alongside human beings in commensal and mutually beneficial relationships. Many physiological processes rely on the microbiota, such as the ability to glean nutrients from complex carbohydrates.
Microbial composition is dependent upon the environment, and as such, each anatomical site on the body contains a characteristic microbiome. Between humans, the microbiota of each body site can be fairly similar. For example, in the gastrointestinal tract, many people will have E. coli present. However, interpersonal variations in diet, disease status, and even mental health are associated with differences in the microbiota between people.
A growing body of literature suggests that differences in microbiota composition exist between healthy individuals and those with disease. For instance, an individual who develops cancer may show an altered microbiota compared to their healthy counterparts. Guerrero-Preston and colleagues demonstrated that individuals with head and neck squamous cell carcinoma (HNSCC) have less diverse microbiota, with increased abundance of the phylum Firmicutes and reduced abundance of Bacteroidetes and Proteobacteria compared to healthy participants .
Dysbiotic events - referring to an unbalanced or homeostatically deviant microbiome that may be triggered by antibiotic use among other factors - can lead to an overgrowth of pathogenic microbes, followed by disease onset. In terms of cancer development and progression, some well-known microbes like F. nucleatum can aid in colorectal cancer establishment and progression via interactions with various immune cells .
Microbial organisms can influence response to cancer therapy. Some microbes, like Lactobacillus plantarum, can facilitate positive chemotherapy response by preventing colorectal cancer cell resistance to 5-fluorouracil, further enabling apoptosis of cancerous cells . Other beneficial microbes can mediate the effects of immunotherapy, and may enhance patient response to treatment. Perhaps by manipulating the microbiome (pro- or prebiotics, fecal transplants, etc.), we can enhance cancer therapeutic efficacy by favoring colonization by microbes that are associated with positive treatment outcomes. Current microbiome research indeed suggests the potential utility of the microbiome to the clinical setting.
Dr. Pierce’s Research
Understanding how the microbiome is correlated to positive or negative treatment outcomes in cancer patients (be it a causal relationship or otherwise) is understudied. However, exploring these associations could unveil unique microbial biomarkers of treatment response and advance the use of techniques to manipulate microbiome structure to favor positive treatment responses. This is where Dr. Pierce's research is focused. By incorporating epidemiological principles and microbiome science, Dr. Pierce and her team are examining the ways in which the human immune system and the microbiome interact in cancer patients, and how these interactions may be related to various treatment outcomes.
In her largest pilot study, Dr. Pierce and her collaborators at the University of Florida, Kintai Therapeutics, and VastBiome, are examining the associations between the gut microbiome and immune system in patients with non-small cell lung cancer (NSCLC), to better understand the complex ways in which these interactions are associated with patient response to immune checkpoint inhibitor (ICI) therapy. In this study, patients collect fecal specimens using the team’s self-developed at home stool collection kit (see below for more details). Specimens are returned within three days of collection. These fecal samples are processed to isolate various macromolecules, including DNA and RNA, for sequencing to identify the presence/abundance and functional profiles of the microbiota, respectively. Metabolites are identified to build a metabolic profile of the microbiota, too. These data, cumulatively with immunological markers found in blood and clinician determined patient response to immunotherapy treatment, are integrated to paint a holistic picture of the factors correlated to different responses to ICI therapy.
In other pilot studies, both prospective and retrospective, our team has explored the oral microbiome and its relationship to the development of treatment related toxicities in head and neck cancer patients undergoing radiation and chemotherapy; the relationship between tumor infiltrating lymphocyte diversities and fractions with the tumor microbiome in head and neck squamous cell carcinoma; and the relationship between antibiotic use (representative of gut microbial dysbiosis) and immunotherapy response in non-small cell lung cancer patients.
For an overview of Dr. Pierce's at-home stool collection kit, click here.
Dr. Pierce and her team developed an at-home stool collection kit optimized for use in cancer patient populations, with sample collection methods conducive to downstream metagenomics analyses. In large epidemiological studies of the microbiome, it is unrealistic to collect fecal samples in a clinical setting - we cannot expect patients to 'poop on command.' Collection at home, while it does address this issue, introduces other logistical concerns. The gold standard for fecal specimen preservation for microbiome analyses is immediate freezing at -80 degrees Celsius, to which at home stool collection is not amenable. At home collection requires preservatives to ensure the structure of the microbiome is not altered between the time of collection and the time at which the specimen can be stored at this low temperature. Dr. Pierce's stool collection kit was developed to ensure stool collection could be completed aseptically, and easily, in the home whilst preserving microbial integrity. Our team recently published the instructions for assembly and use of this stool collection kit in the journal Microbial Ecology:
To view our team's most recent publication that outlines the procedure for assembly and use of our at-home stool collection kit, click on the link: Hogue S, Gomez M, Vieira da Silva W, Pierce CM. A customized at-home stool collection protocol for use in microbiome studies conducted in cancer patient populations. Microb Ecol 2019 In Press.
Studies of the microbiome require the use of sequencing techniques to capture the presence of microorganisms that would otherwise be missed in culturing techniques. This allows microbiome scientists to achieve in depth profiles of the bacteria and other microorganisms present in a specimen, regardless of whether the organism is culturable.
Explore how our team has used two major sequencing technologies to uncover the composition of the microbiome and TIL repertoires of various tumor tissues and other samples.
Guerrero-Preston, R., et al., 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment. Oncotarget, 2016. 7(32): p. 51320-51334.
Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, Clancy TE, Chung DC, Lochhead P, Hold GL, El-Omar EM, Brenner D, Fuchs CS, Meyerson M, Garrett WS (2013) Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14 (2):207-215. doi:10.1016/j.chom.2013.07.007