Major advances in our understanding of the tumor immune microenvironment (TIME) in established cancer have been made, including the influence of host-intrinsic (host genomics) and -extrinsic factors (such as diet and the microbiome) on treatment response. Nonetheless, the immune and microbiome milieu across the spectrum of precancerous tissue and early neoplasia is a growing area of interest. There are emerging data describing the contribution of the immune microenvironment and microbiota on benign and premalignant tissues, with opportunities to target these factors in cancer prevention and interception. Throughout this review, we provide rationale for not only the critical need to further elucidate the premalignant immune microenvironment, but also for the utility of pharmacologic and lifestyle interventions to alter the immune microenvironment of early lesions to reverse carcinogenesis. Novel research methodologies, such as implementing spatial transcriptomics and proteomics, in combination with innovative sampling methods will advance precision targeting of the premalignant immune microenvironment. Additional studies defining the continuum of immune and microbiome evolution, which emerges in parallel with tumor development, will provide novel opportunities for cancer interception at the earliest steps in carcinogenesis.

Carcinogenesis is typically defined as the process by which normal cells transform into tumor cells through acquiring characteristics that confer a survival advantage. In addition, the term also represents a coevolution of the immediate cellular environment, including the immune infiltrate, surrounding microbes, stroma, and vasculature. In many tumor types, the progression from normal tissue to invasive malignancy has been extensively studied and characterized, detailing the genomic, transcriptomic, proteomic, and epigenomic changes within tumor cells across the spectrum of carcinogenesis. Further, many studies exist on describing the tumor immune microenvironment (TIME) in established cancer, as well as microbial changes associated with advanced cancer and therapy response. Fewer studies, however, have documented the parallel changes within the immune microenvironment or microbiome during carcinogenesis, which simultaneously progress towards an overwhelmingly immunosuppressive and dysbiotic phenotype. This coevolution is a dynamic process with intricate communication between the developing tumor cells, the local and systemic immune system, as well as components of the gut and regional tissue microbiome (graphical depiction in Fig. 1).

Figure 1.

Mechanisms by which the immune and microbial microenvironments promote carcinogenesis. In parallel with histologic progression from healthy tissue to precancerous lesion and invasive cancer, tumor cell–intrinsic (purple) and -extrinsic (blue and yellow) factors coevolve toward a protumorigenic phenotype. Accordingly, opportunity for effective microenvironment-targeted interception decreases through carcinogenesis. (Created with BioRender.com.)

Figure 1.

Mechanisms by which the immune and microbial microenvironments promote carcinogenesis. In parallel with histologic progression from healthy tissue to precancerous lesion and invasive cancer, tumor cell–intrinsic (purple) and -extrinsic (blue and yellow) factors coevolve toward a protumorigenic phenotype. Accordingly, opportunity for effective microenvironment-targeted interception decreases through carcinogenesis. (Created with BioRender.com.)

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This review focuses on the contribution of local and systemic changes to the immune response and microbiome in premalignancy, with sections addressing (i) tumor–immune crosstalk during carcinogenesis, (ii) evolution of immune microenvironment during premalignancy, (iii) the interplay of the immune milieu and microbiome in precancerous lesions, (iv) the influence of risk factors and risk-reducing interventions, (v) translational research opportunities for defining the immune microenvironment in premalignancy, and (vi) future research opportunities. We review the promising application of immune- and microbiome-targeting therapies for cancer prevention as well as point out critical knowledge gaps that remain.

Oncogenic pathway activation – through gain-of-function alterations of oncogenes or loss-of-function of tumor suppressor genes – has historically defined the earliest stages of cancer development. Driver mutations in oncogenes and tumor suppressor genes were initially assumed to modulate cell-intrinsic processes only. However, these factors dramatically affect cell-extrinsic processes, including the antitumor immune response. Cross-talk between driver mutations in tumor cells and the immune environment occurs with multiple oncogenic pathways, including Myc, β-catenin, PTEN, and many others. Myc and its related signaling pathways are among the most commonly mutated oncogenes in human cancer, driving uncontrolled cell division. Myc, however, also regulates the immune microenvironment via reducing antigen presentation (decreased MHC I and II expression), limiting immune-mediated killing by macrophages and natural killer (NK) cells, and preventing T-cell infiltration (1, 2). Myc activation in preclinical pancreatic cancer models also induces rapid recruitment of mast cells, which are necessary for tumor growth (3). β-Catenin signaling is disrupted in many tumor types, including melanoma and colorectal cancer. Alongside its roles in cell proliferation and migration, β-catenin signaling also represses immune cell activation by preventing infiltration of BATF+ dendritic cells (DC), which are critical in priming naïve T cells, and by inhibiting T-cell recruitment (2). A final example of crosstalk between driver mutations in tumor cells and the immediate immune environment is that of PTEN loss, which occurs early in the development of many tumor types. In preclinical prostate cancer models, PTEN loss results in MDSC recruitment and the shifting of cytokines and inflammatory modulators towards an immunosuppressive phenotype (4). PTEN loss can promote NF-κB activation during pancreatic ductal adenocarcinoma (PDAC) development (5). PTEN loss also modifies the composition of infiltrating immune cells in the pretumor microenvironment, including increases in protumorigenic macrophages in liver cancer development (6) and reductions of CD8+ T cells in melanoma (7).

Accumulation of somatic mutations and DNA copy-number alterations during tumor development also affects antitumor immune responses. Point and frameshift mutations are a primary source of tumor neoantigens, which are recognized by the host immune system and can facilitate immune-mediated tumor cell killing. However, progressive chromosomal aberrations and aneuploidy is associated with decreased adaptive and innate immune cell infiltration, decreased ratios of CD8+:CD4+ T cells and M1:M2 macrophages, and decreased expression of cytolytic proteins and IFN signaling (8).

Preclinical work continues to identify novel ways in which driver mutations and chromosomal aberrations impact antitumor immune activity. Coculture systems of tumor cells and isolated CD8+ T cells have been employed to identify novel genes that confer resistance of tumor cells to cytotoxic T cells in vitro (9). In addition, comparisons of immunodeficient versus wild-type mice have identified many novel tumor suppressor genes specific to modulation of immune activity (10). The sheer number of novel genetic elements identified in these studies suggests that our view of the coevolution of tumor cells and the immune system remains quite naïve, necessitating additional studies to increase understanding of the sophisticated crosstalk between tumor cells and immune microenvironment during cancer development.

Although oncogenic signaling pathways generally stimulate immune activation early in malignant transformation, the transition to evasion of antitumor immune response is a Hallmark of Cancer (11). Translational studies have demonstrated evidence of both immune activation and evasion at the premalignant state, prior to invasion.

In both lung and oral squamous cell carcinoma (SCC), detailed transcriptional and histologic analyses along the carcinogenesis spectrum have allowed longitudinal assessment of immune involvement, revealing marked changes in immune activity prior to tumor invasion. Neutrophils and naïve T cells dominate the immune microenvironment early in lung SCC development, in association with high cancer neoantigen expression (12). High-grade lesions exhibit increased T-cell activation prior to invasion, then express markers of T-cell exhaustion during the transition from in situ disease to invasive carcinoma. Moreover, expression of antitumor immune response genes decreases during epithelial–mesenchymal transition (EMT; ref. 12). In oral SCC, early lesions exhibit high levels of tumor-infiltrating lymphocytes. Some of these early lesions spontaneously regress, suggesting an active antitumor immune response. Lesions that progress to oral SCC, rather, exhibit increases in immune checkpoint expression and in infiltrating immunosuppressive cell types, including MDSCs, M2 macrophages, and regulatory T cells (Tregs ref. 13).

Similarly, progressive downregulation of immune activation pathways alongside upregulation of immunosuppressive pathways occurs during adenocarcinoma development. Parallel histologic studies exhibit decreased infiltration of cytotoxic and Th cells and increased infiltration of Tregs during the progression to preinvasive and early lung adenocarcinoma (14). A longitudinal cohort study of patients with the premalignant breast cancer lesion ductal carcinoma in situ (DCIS) determined that features associated with immune activation, such as CD4+ T-cell and mast cell infiltration, were observed primarily in DCIS and not invasive breast cancer lesions (15).

Evidence of decreased immune activation with concurrent increases in immunosuppressive factors at the earliest stages of carcinogenesis, prior to overt invasion, implies that immune activation and evasion occur in the premalignant state. These data suggest that earlier immunomodulatory treatment strategies might be not only feasible but potentially more efficacious than in the more deranged immune microenvironment of advanced malignancy. Further work in understanding the immune response in premalignant lesions is critical to address these gaps in knowledge.

There is an ever-growing appreciation for the role of the microbiome in cancer – from the earliest steps in carcinogenesis all the way to metastasis. We focus here on the beginning of tumor formation and outline evidence for a continuum of microbial changes that parallel transformation of tumor cells and the tumor immune microenvironment. Whereas various viruses and bacteria have been elucidated as causative agents in multiple cancers (e.g., H. pylori-associated gastric cancers and human papillomavirus (HPV)-associated cervical, oral, and anal cancers), it is becoming increasingly evident that commensal microbiota further shape tumorigenesis and the antitumor immune response. As an example, although H. pylori is associated with gastric cancer, H. pylori infection does not cause cancer in most patients, suggesting that other factors modify its carcinogenic activities. H. pylori infection is associated with gastric dysbiosis, specifically with decreased abundance and variety of other microbes present in the uninfected state (16). Moreover, in preclinical models, germ-free mice infected with H. pylori develop gastric intraepithelial neoplasia less often and more slowly than conventional mice or mice with a restricted microbiome (16). These data suggest that components of the gastric microbiome other than H. pylori may synergize in gastric carcinogenesis. Similarly, while HPV is a known causative agent for both cervical intraepithelial neoplasia (CIN) and cervical cancer, only a small fraction of infected women has persistent HPV infection and develops lesions. The cervicovaginal microbiome may alter the ability of HPV to persist and cause infection. In fact, a signature of cervicovaginal microbiome consisting of increased diversity of microbiota, increased Gardnerella spp., and reduced Lactobacillus spp. is associated with development of cervical premalignant lesions (17, 18). Furthermore, researchers identified a bacterial signature in the perianal region linked with higher-risk HPV-related precancerous anal intraepithelial neoplastic lesions more likely to progress to carcinoma (19).

Microbes influence cancer development via both direct and indirect roles. The premalignant tissue-resident bacteria have been explored in greatest depth for gastrointestinal cancers. In colorectal cancer, differences in the microbiome are associated with serrated versus adenomatous colorectal carcinogenic pathway. Increases in microbial richness, diversity, and specific species are apparent in adenomatous lesions compared with normal colonic tissue (20). Biofilms, associated with bacterial overgrowth and invasion, are found in right-sided colonic tumors, premalignant adenomas, and adjacent normal tissue, suggesting that they may play a role in early-tumor formation (21). Patients suffering from chronic gastritis or other gastric preneoplastic lesions have altered gastric pH, which facilitates survival of some oral bacteria and other intestinal commensals, particularly nitrosating bacteria, which can have genotoxic effects (22). Indeed, the microbiome of patients with premalignant gastric lesions, when transplanted into germ-free mice, induced gastric dysplasia (23). Gut microbes even exhibit the ability to hijack hormone signaling, where gut dysbiosis induces changes to estrogen metabolism (24) and production of androgens during prostate cancer development (25), which may tune cancer development both locally or distantly. Further, cross-talk between the immune microenvironment and microbiome facilitate oncogenesis. In PDAC, an influx of bacterial colonization from the stomach to the pancreas reprograms the developing tumor microenvironment towards an immunosuppressive phenotype (26). In additon, intratumoral bacteria, which are present inside tumor cells and local immune cells, vary among tumor types (including those outside the gut) in both diversity and metabolic profile, suggesting their roles in cancer–immune signaling (27). However, comprehensive analyses of intratumor microbiomes across tissue types are lacking for premalignant lesions, especially those beyond the digestive system.

Although the role of the fungal microbiome is not yet well-defined, very recent studies demonstrate its potential to influence carcinogenesis across multiple cancer types. Large pan-cancer sequencing studies identified fungal signatures associated with gastrointestinal cancer development (28, 29). In pancreatic cancer, activation of the fungal complement cascade via mannose-binding lectin is required for oncogenesis (30). Also in pancreatic cancer, oncogenic Kras has been found to increase IL33 expression, which is dependent on the intratumoral mycobiome and can be modulated via antifungal treatment (31). In oral premalignant lesions, those associated with Candidal infection were more likely to progress to oral SCC, and clearance of Candida leads to regression in some patients. However, whether Candida causes or is merely associated with oral premalignancy is not known and may depend on other factors, such as immune activity and general dysbiosis (32). Additional studies across the cancer development continuum are necessary to decipher the distinct roles of commensal versus pathogenic fungi in carcinogenesis.

Commensal microbes, the symbiotic bacteria that normally play a role in host defense and digestion, have the capacity to influence cancer initiation systemically as well as locally, via mechanisms distinct from intratumoral bacteria. Commensal microbes secrete factors that regulate hormone-producing cells and immune cells. For example, microbe-mediated hormone release occurs in the gut, whereby commensals influence the release of various gastrointestinal hormones (including CCK, PYY, GLP-1, GIP, and 5-HT) by enteroendocrine cells, which have systemic effects on insulin sensitivity, glucose tolerance, and other metabolic functions (reviewed in ref. 33). Moreover, the gut microbiome influences the immune system by either signaling to local immune cells within the lamina propria or nearby lymphoid tissues (reviewed in ref. 34), or by releasing metabolites (such as short chain fatty acids, amino acids, and bile acids) into the circulation. For example, short-chain fatty acids activate peripheral Tregs (35–37) with mainly immunosuppressive effects. Distinct systemic cancer-related microbial signatures have also been identified in blood versus tissue signature studies from The Cancer Genome Atlas (TCGA), and in fact revealed the utility of liquid biopsy of microbial signatures for cancer detection (38). However, a knowledge gap still exists on the influence of commensals in cancer development specifically, as well as distinctions between the impact of commensal versus intratumoral microbes on cancer development beyond those in and around the digestive system. These and aforementioned data signify the influence of the microbiome on early-stages of carcinogenesis and support the use of microbial signatures as biomarkers for high-risk lesions. Moreover, these findings indicate the potential utility for microbial intervention in cancer interception.

Thus far, strategies to alter the anti-tumor immune response or cancer-associated dysbiosis have typically been employed after diagnosis of overt malignant disease, often in the setting of advanced or even metastatic cancer. Evidence of the immune and microbial influence in early carcinogenesis underscores the importance of evaluating the influence of risk factors and risk-reducing interventions in modulating the immune microenvironment and microbiome to reverse disease progression. Here, we will specifically focus on obesity, inflammation, and hereditary cancer risk.

Obesity is a multifactorial disorder, characterized by chronic systemic and local inflammation, metabolic dysfunction, and microbial dysbiosis, all of which contribute to immunosuppression during carcinogenesis. For example, in preclinical models, obesity promotes inflammation and immunosuppression within the liver, permitting obesity-related hepatocellular carcinogenesis. Obesity-induced gut microbial COX2 signaling causes PGE2 production in hepatic stellate cells, which suppresses antitumor immunity during carcinogenesis via modulation of local cytokine expression (39). The inflammatory state in obesity promotes leakage of microbial metabolites into the portal circulation (gut–liver axis), further amplifying inflammation within the liver. Obesity-related gut dysbiosis has been implicated in other cancer development processes, including in endometrial cancer, where obesity- and menopause-related gut dysbiosis affect estrogen metabolism and promote recruitment of Tregs to the endometrium (40). Obesity similarly affects the vaginal and uterine microbiome (41), where dysbiosis, including reduced diversity and changes to the dominant microbial species, has been observed early during endometrial carcinogenesis (42). Obesity impacts the immune system in endometrial cancer risk also. Obese women who prospectively underwent bariatric surgery for weight loss (with predicted endometrial cancer risk reduction) subsequently had decreased systemic inflammatory biomarkers (CRP, IL6) and increased endometrial infiltration of CD8+ T cells (43). Finally, obesity has been shown to affect not only the proportion of immune cell types in the microenvironment but also their function. Secondary to metabolic dysfunction in obesity, competition for lipids in the immune microenvironment causes CD8+ T-cell dysfunction (44).

Inflammation also modulates cancer development via the immune microenvironment in other chronic conditions. In inflammatory bowel disease (IBD), chronic inflammation induces both dysbiosis and an immunosuppressive microenvironment. Inflammatory insults to intestinal barrier integrity (45) cause an influx of microbes, often from a dysbiotic background, into tissues at risk of cancer development (46). Chronic inflammation in ulcerative colitis is characterized by increased TNFα signaling (47), IL6-dependent STAT3 activation (48, 49), and Th17 cell infiltration (50), all of which contribute to proinflammatory, protumorigenic signaling. Furthermore, activation of innate immunity plays a dual role in colitis-associated carcinogenesis: while activation of innate immunity has been shown to protect against colitis-associated carcinogenesis, it also contributes further to proinflammatory, protumorigenic signaling within ulcerative colitis lesions (51). In Barrett's esophagus, premalignant lesions characterized by chronic inflammation, increased IL6 and CXCL8 production alongside higher numbers of M2 macrophages, pro-B cells, and eosinophils are associated with progression to esophageal adenocarcinoma (52). Controlling inflammation via surgical or pharmacologic intervention in these chronic diseases can prevent malignancy (53, 54).

Genetic predisposition for cancer is a nonmodifiable risk factor yet represents a unique opportunity for immune-based cancer interception strategies. Lynch syndrome, or hereditary nonpolyposis colorectal cancer syndrome (HNPCC), is caused by inherited loss of DNA mismatch repair genes. Resultant accumulation of mutations due to defective DNA repair increases the risk for developing colorectal, endometrial, and ovarian cancers (55). Hypermutability also causes production of neoantigens, frame-shift peptides recognized by the immune system (56). Importantly, immune reactivity to cancer-related neoantigens precedes evidence of even histologic premalignant (adenomatous polyp) transformation (57). Intervention at early stages in carcinogenesis has the potential to prevent cancer development. The NSAID naproxen exhibits efficacy against colorectal cancer development in part due to its effects on the immune system, by the activation of T and B cells (without altering the number of infiltrating immune cells) (58). These findings have led to increased interest in developing precision immune interception strategies against cancer development in patients with Lynch syndrome, including neoantigen-targeted vaccines (59).

Leveraging the precancerous immune and microbial microenvironment against cancer development has the potential to revolutionize cancer prevention strategies, especially for patients with known risk factors, such as obesity, chronic inflammatory conditions or infections, and genetic predisposition. Immuno-preventive strategies, including vaccination and immunotherapy, are discussed elsewhere in this series, but opportunities also exist for lifestyle modification in harnessing the potential of the immune and microbial microenvironment against cancer development. Many studies focus on the modulatory effects of dietary changes on antitumor immune activity and the microbiome in patients that already have invasive cancer, where a high-fiber diet has been shown to enhance response to immune checkpoint blockade via modulation of the gut microbiome (60). Preclinical studies have demonstrated the utility of probiotic use for colorectal cancer prevention, where various probiotics (Clostridium butyricum, Bacillus subtilis, Lactobacillus rhamnosus, or a cocktail of Lactobacillus acidophilus, Bifidobacteria bifidum, and Bifidobacteria infantum) show potential prophylactic effect against an inflammatory model of colorectal cancer development (61–63). Pre- and pro-biotic supplementation with a preparation of oligofructose-enriched inulin, Lactobacillus rhamnosus GG, and Bifidobacterium lactis Bb12, also decreased genotoxicity and reduced IL2 production by peripheral blood mononuclear cells in patients with precancerous colonic lesions in a randomized controlled trial (64). However, in the setting of cancer recurrence, dietary fiber (wheat bran) and/or probiotic supplementation (Lactobacillus casei) does not appear to have the same protective effect (65), supporting the notion that lifestyle modification in the precancerous stage may have the most significant impact.

Several clinical trials evaluating the impact of microbiome modulation on cancer prevention have launched. Such trials include the effect of dietary interventions on commensal microbiome and subsequent impact on colorectal cancer prevention in patients at increased risk due to obesity (NCT02843425, NCT03582306) or lung cancer in patients at increased risk due to significant smoking history (NCT04267874). As an example, the ongoing BE GONE trial (66) implements the addition of one cup of canned beans per day to each participant’s typical diet as a preventive approach for overweight and obese patients with a history of colorectal polyps or cancer (primary objective is evaluation of gut microbiome plus blood adipokine and cytokine biomarkers). This trial builds from both human and rodent models that show anti-inflammatory and chemopreventive influence of beans (67–69), including a trial (NCT01929122) which showed rice bran or navy bean interventions increase microbial diversity and alter microbiome composition after 28 days (70). An alternative approach evaluated providing participants with frozen dark leafy green vegetables in 1 cup “doses” daily in addition to their typical diet (NCT03582306), and has demonstrated feasibility for accrual, retention, and acceptability (primary outcomes), but secondary outcomes (microbiome composition, DNA damage, and inflammatory biomarker studies) are pending. In the BE WELL lung cancer trial (NCT04267874) the effects of black raspberry nectar powder on microbiome and inflammation markers, but results have not yet been reported. Other trials evaluating microbiome modulation with non-dietary interventions include the use of metformin for prevention of cancer in patients with oral precancerous lesions (NCT02581137) and omega-3 polyunsaturated fatty acid supplementation in participants with a history of colorectal adenoma (NCT04216251). These trials, while providing valuable clinical information on the impact of targeting the microenvironment for cancer prevention, will also have the added opportunities for tissue-based studies to increase understanding of the determinants for immune- and microbiome-based cancer interception.

Broad interest and enthusiasm for cancer immunotherapy research has not yet transferred to the premalignant setting, which may be more tractable for immune-based interventions. Cancers with a well-characterized preneoplastic lesion, accessible tissue location, and well-defined risk factors are an ideal setting to define the role of immune response and immunoprevention for cancer interception. In the past, limited tissue availability, small lesion size, and substantial regional heterogeneity have proven challenging for translational research in the premalignant setting. While local heterogeneity in immune infiltrate and oncogenic signaling can drive either regression or progression of precancerous lesions, it has been difficult to define these interactions. Recently, however, methodologic advances provide ample opportunities in this realm. Analysis of regional variation had not previously benefited from deep profiling due to platforms that lacked spatial resolution. However, novel methods, such as spatial transcriptomics and/or proteomics, allow dissection of regional crosstalk between oncogenic signaling pathways and the immune microenvironment, which is a particularly powerful approach for small or otherwise limited precursor lesions. Furthermore, evaluation of regional microbes and local immune signaling with spatial resolution will enable interrogation of the crosstalk between key signaling pathways that drive the progression or regression of premalignant lesions. Advances in methodology for assessing the immune and microbiome microenvironment of precancerous lesions will be complemented by novel screening techniques for precursor lesions, including liquid biopsy (its application to cancer prevention reviewed in ref. 71), nanoparticle-directed imaging modalities (reviewed in ref. 72), and microfluidic nanochip-based detection of tumor-specific exosomes (73). These novel screening techniques will further advance cancer interception by allowing for earlier detection. Identification of lesions early in carcinogenesis, along with insight on the composition of the pretumor microenvironment, will inform the utility of immune and microbiome targeting for cancer interception.

Traditional approaches to cancer interception have attempted to target specific oncogenic signaling pathways but have had limited uptake in at-risk populations. New cancer interception strategies focused on the immune microenvironment and the microbiome may enable broader applications due to the potential for intermittent interventions to support antitumor immune response and relevance across multiple tissue/tumor types. Importantly, enhanced pharmacologic approaches are being partnered with cancer interception agents (overview included in ref. 74), which could support efficacy of local immune modulation. Alternatively, multi-organ cancer interception strategies with potential to improve multiple morbidities associated with cancer risk factors (such as obesity or chronic inflammation) will also have the greatest likelihood of a favorable cost/benefit ratio. While dietary interventions have been studied for cancer prevention for decades, the recent understanding of the role of fiber and other dietary modifications in modifying the gut microbiome and response to immunotherapy (60, 75, 76) provides a new paradigm, including new potential biomarkers and routes for modulation. Given the well-recognized role of the microbiome in cancer development and progression, along with many remaining knowledge gaps, future study designs and specimen collection procedures must incorporate appropriate techniques to enable analysis of the tissue and gut microbiome with necessary rigor. Although earlier large-scale studies leveraged existing specimens and sequencing data to interrogate the intratumoral microbiome in an opportunistic manner, prospective sampling of gut and tissue microbiome will enable critical advances, particularly for premalignant conditions and at-risk patient populations. As mentioned above, spatial biology techniques will enable powerful opportunities for integration of microbiome analyses into multi-platform profiling studies.

J.A. Wargo reports personal fees from Imedex, Dava Oncology, Omniprex, Illumina, Gilead, PeerView, Physician Education Resource, MedImmune, Exelixis, and personal fees from Bristol Myers Squibb outside the submitted work; in addition, J.A. Wargo has a patent for PCT/US17/53.717 issued and has served as a consultant/advisory board member for Roche/Genentech, Novartis, AstraZeneca, GlaxoSmithKline, Bristol Myers Squibb, Micronoma, OSE therapeutics, Merck, and Everimmune. J.A. Wargo received stock options from Micronoma and OSE therapeutics. No disclosures were reported by the other authors.

The content is solely the responsibility of the authors and does not necessarily represent the official views of the funders.

M.B. Bowen was supported by a predoctoral fellowship from the Cancer Prevention and Research Institute of Texas (RP210042). All authors were supported by the Cancer Center Support Grant at MD Anderson Cancer Center (CA016672).

1.
Dhanasekaran
R
,
Deutzmann
A
,
Mahauad-Fernandez
WD
,
Hansen
AS
,
Gouw
AM
,
Felsher
DW
.
The MYC oncogene - the grand orchestrator of cancer growth and immune evasion
.
Nat Rev Clin Oncol
2022
;
19
:
23
36
.
2.
Spranger
S
,
Gajewski
TF
.
Impact of oncogenic pathways on evasion of antitumour immune responses
.
Nat Rev Cancer
2018
;
18
:
139
47
.
3.
Soucek
L
,
Lawlor
ER
,
Soto
D
,
Shchors
K
,
Swigart
LB
,
Evan
GI
.
Mast cells are required for angiogenesis and macroscopic expansion of Myc-induced pancreatic islet tumors
.
Nat Med
2007
;
13
:
1211
8
.
4.
Garcia
AJ
,
Ruscetti
M
,
Arenzana
TL
,
Tran
LM
,
Bianci-Frias
D
,
Sybert
E
, et al
.
Pten null prostate epithelium promotes localized myeloid-derived suppressor cell expansion and immune suppression during tumor initiation and progression
.
Mol Cell Biol
2014
;
34
:
2017
28
.
5.
Ying
H
,
Elpek
KG
,
Vinjamoori
A
,
Zimmerman
SM
,
Chu
GC
,
Yan
H
, et al
.
PTEN is a major tumor suppressor in pancreatic ductal adenocarcinoma and regulates an NF-kappaB-cytokine network
.
Cancer Discov
2011
;
1
:
158
69
.
6.
Debebe
A
,
Medina
V
,
Chen
CY
,
Mahajan
IM
,
Jia
C
,
Fu
D
, et al
.
Wnt/beta-catenin activation and macrophage induction during liver cancer development following steatosis
.
Oncogene
2017
;
36
:
6020
9
.
7.
Peng
W
,
Chen
JQ
,
Liu
C
,
Malu
S
,
Creasy
C
,
Tetzlaff
MT
, et al
.
Loss of PTEN promotes resistance to T cell-mediated immunotherapy
.
Cancer Discov
2016
;
6
:
202
16
.
8.
Davoli
T
,
Uno
H
,
Wooten
EC
,
Elledge
SJ
.
Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy
.
Science
2017
;
355
:
eaaf8399
.
9.
Lawson
KA
,
Sousa
CM
,
Zhang
X
,
Kim
E
,
Akthar
R
,
Caumanns
JJ
, et al
.
Functional genomic landscape of cancer-intrinsic evasion of killing by T cells
.
Nature
2020
;
586
:
120
6
.
10.
Martin
TD
,
Patel
RS
,
Cook
DR
,
Choi
MY
,
Patil
A
,
Liang
AC
, et al
.
The adaptive immune system is a major driver of selection for tumor suppressor gene inactivation
.
Science
2021
;
373
:
1327
35
.
11.
Hanahan
D
,
Weinberg
RA
.
Hallmarks of cancer: the next generation
.
Cell
2011
;
144
:
646
74
.
12.
Mascaux
C
,
Angelova
M
,
Vasaturo
A
,
Beane
J
,
Hijazi
K
,
Anthoine
G
, et al
.
Immune evasion before tumour invasion in early lung squamous carcinogenesis
.
Nature
2019
;
571
:
570
5
.
13.
Rangel
R
,
Pickering
CR
,
Sikora
AG
,
Spiotto
MT
.
Genetic changes driving immunosuppressive microenvironments in oral premalignancy
.
Front Immunol
2022
;
13
:
840923
.
14.
Dejima
H
,
Hu
X
,
Chen
R
,
Zhang
J
,
Fujimoto
J
,
Parra
ER
, et al
.
Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features
.
Nat Commun
2021
;
12
:
2722
.
15.
Risom
T
,
Glass
DR
,
Averbukh
I
,
Liu
CC
,
Baranski
A
,
Kagel
A
, et al
.
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma
.
Cell
2022
;
185
:
299
310
.
16.
Lofgren
JL
,
Whary
MT
,
Ge
Z
,
Muthupalani
S
,
Taylor
NS
,
Mobley
M
, et al
.
Lack of commensal flora in Helicobacter pylori-infected INS-GAS mice reduces gastritis and delays intraepithelial neoplasia
.
Gastroenterology
2011
;
140
:
210
20
.
17.
Norenhag
J
,
Du
J
,
Olovsson
M
,
Verstraelen
H
,
Engstrand
L
,
Brusselaers
N
.
The vaginal microbiota, human papillomavirus and cervical dysplasia: a systematic review and network meta-analysis
.
BJOG
2020
;
127
:
171
80
.
18.
Usyk
M
,
Zolnik
CP
,
Castle
PE
,
Porras
C
,
Herrero
R
,
Gradissimo
A
, et al
.
Cervicovaginal microbiome and natural history of HPV in a longitudinal study
.
PLoS Pathog
2020
;
16
:
e1008376
.
19.
Ron
R
,
Cabello
A
,
Gosalbes
MJ
,
Sanchez-Conde
M
,
Talavera-Rodriguez
A
,
Zamora
J
, et al
.
Exploiting the microbiota for the diagnosis of anal precancerous lesions in men who have sex with men
.
J Infect Dis
2021
;
224
:
1247
56
.
20.
DeDecker
L
,
Coppedge
B
,
Avelar-Barragan
J
,
Karnes
W
,
Whiteson
K
.
Microbiome distinctions between the CRC carcinogenic pathways
.
Gut Microbes
2021
;
13
:
1854641
.
21.
Dejea
CM
,
Wick
EC
,
Hechenbleikner
EM
,
White
JR
,
Mark Welch
JL
,
Rossetti
BJ
, et al
.
Microbiota organization is a distinct feature of proximal colorectal cancers
.
Proc Natl Acad Sci U S A
2014
;
111
:
18321
6
.
22.
Bessede
E
,
Megraud
F
.
Microbiota and gastric cancer
.
Semin Cancer Biol
2022
;
86
(
Pt 3
):
11
7
.
23.
Kwon
SK
,
Park
JC
,
Kim
KH
,
Yoon
J
,
Cho
Y
,
Lee
B
, et al
.
Human gastric microbiota transplantation recapitulates premalignant lesions in germ-free mice
.
Gut
2022
;
71
:
1266
76
.
24.
Ervin
SM
,
Li
H
,
Lim
L
,
Roberts
LR
,
Liang
X
,
Mani
S
, et al
.
Gut microbial beta-glucuronidases reactivate estrogens as components of the estrobolome that reactivate estrogens
.
J Biol Chem
2019
;
294
:
18586
99
.
25.
Pernigoni
N
,
Zagato
E
,
Calcinotto
A
,
Troiani
M
,
Mestre
RP
,
Cali
B
, et al
.
Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis
.
Science
2021
;
374
:
216
24
.
26.
Pushalkar
S
,
Hundeyin
M
,
Daley
D
,
Zambirinis
CP
,
Kurz
E
,
Mishra
A
, et al
.
The pancreatic cancer microbiome promotes oncogenesis by induction of innate and adaptive immune suppression
.
Cancer Discov
2018
;
8
:
403
16
.
27.
Nejman
D
,
Livyatan
I
,
Fuks
G
,
Gavert
N
,
Zwang
Y
,
Geller
LT
, et al
.
The human tumor microbiome is composed of tumor type-specific intracellular bacteria
.
Science
2020
;
368
:
973
80
.
28.
Dohlman
AB
,
Klug
J
,
Mesko
M
,
Gao
IH
,
Lipkin
SM
,
Shen
X
, et al
.
A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors
.
Cell
2022
;
185
:
3807
22
.
29.
Narunsky-Haziza
L
,
Sepich-Poore
GD
,
Livyatan
I
,
Asraf
O
,
Martino
C
,
Nejman
D
, et al
.
Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions
.
Cell
2022
;
185
:
3789
806
.
30.
Aykut
B
,
Pushalkar
S
,
Chen
R
,
Li
Q
,
Abengozar
R
,
Kim
JI
, et al
.
The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL
.
Nature
2019
;
574
:
264
7
.
31.
Alam
A
,
Levanduski
E
,
Denz
P
,
Villavicencio
HS
,
Bhatta
M
,
Alhorebi
L
, et al
.
Fungal mycobiome drives IL-33 secretion and type 2 immunity in pancreatic cancer
.
Cancer Cell
2022
;
40
:
153
67
.
32.
Hongal
BP
,
Kulkarni
VV
,
Deshmukh
RS
,
Joshi
PS
,
Karande
PP
,
Shroff
AS
.
Prevalence of fungal hyphae in potentially malignant lesions and conditions-does its occurrence play a role in epithelial dysplasia?
J Oral Maxillofac Pathol
2015
;
19
:
10
7
.
33.
Martin
AM
,
Sun
EW
,
Rogers
GB
,
Keating
DJ
.
The influence of the gut microbiome on host metabolism through the regulation of gut hormone release
.
Front Physiol
2019
;
10
:
428
.
34.
Gopalakrishnan
V
,
Helmink
BA
,
Spencer
CN
,
Reuben
A
,
Wargo
JA
.
The influence of the gut microbiome on cancer, immunity, and cancer immunotherapy
.
Cancer Cell
2018
;
33
:
570
80
.
35.
Atarashi
K
,
Tanoue
T
,
Oshima
K
,
Suda
W
,
Nagano
Y
,
Nishikawa
H
, et al
.
Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota
.
Nature
2013
;
500
:
232
6
.
36.
Arpaia
N
,
Campbell
C
,
Fan
X
,
Dikiy
S
,
van der Veeken
J
., deRoos P, et al
.
Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation
.
Nature
2013
;
504
:
451
5
.
37.
Furusawa
Y
,
Obata
Y
,
Fukuda
S
,
Endo
TA
,
Nakato
G
,
Takahashi
D
, et al
.
Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells
.
Nature
2013
;
504
:
446
50
.
38.
Poore
GD
,
Kopylova
E
,
Zhu
Q
,
Carpenter
C
,
Fraraccio
S
,
Wandro
S
, et al
.
Microbiome analyses of blood and tissues suggest cancer diagnostic approach
.
Nature
2020
;
579
:
567
74
.
39.
Loo
TM
,
Kamachi
F
,
Watanabe
Y
,
Yoshimoto
S
,
Kanda
H
,
Arai
Y
, et al
.
Gut microbiota promotes obesity-associated liver cancer through PGE(2)-mediated suppression of antitumor immunity
.
Cancer Discov
2017
;
7
:
522
38
.
40.
Schreurs
MPH
,
de Vos van Steenwijk
PJ
,
Romano
A
,
Dieleman
S
,
Werner
HMJ
.
How the gut microbiome links to menopause and obesity, with possible implications for endometrial cancer development
.
J Clin Med
2021
;
10
:
2916
.
41.
Walsh
DM
,
Hokenstad
AN
,
Chen
J
,
Sung
J
,
Jenkins
GD
,
Chia
N
, et al
.
Postmenopause as a key factor in the composition of the Endometrial Cancer Microbiome (ECbiome)
.
Sci Rep
2019
;
9
:
19213
.
42.
Walther-Antonio
MR
,
Chen
J
,
Multinu
F
,
Hokenstad
A
,
Distad
TJ
,
Cheek
EH
, et al
.
Potential contribution of the uterine microbiome in the development of endometrial cancer
.
Genome Med
2016
;
8
:
122
.
43.
Naqvi
A
,
MacKintosh
ML
,
Derbyshire
AE
,
Tsakiroglou
AM
,
Walker
TDJ
,
McVey
RJ
, et al
.
The impact of obesity and bariatric surgery on the immune microenvironment of the endometrium
.
Int J Obes (Lond)
2022
;
46
:
605
12
.
44.
Ringel
AE
,
Drijvers
JM
,
Baker
GJ
,
Catozzi
A
,
Garcia-Canaveras
JC
,
Gassaway
BM
, et al
.
Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity
.
Cell
2020
;
183
:
1848
66
.
45.
Wang
F
,
Schwarz
BT
,
Graham
WV
,
Wang
Y
,
Su
L
,
Clayburgh
DR
, et al
.
IFN-gamma-induced TNFR2 expression is required for TNF-dependent intestinal epithelial barrier dysfunction
.
Gastroenterology
2006
;
131
:
1153
63
.
46.
Uronis
JM
,
Muhlbauer
M
,
Herfarth
HH
,
Rubinas
TC
,
Jones
GS
,
Jobin
C
.
Modulation of the intestinal microbiota alters colitis-associated colorectal cancer susceptibility
.
PLoS One
2009
;
4
:
e6026
.
47.
Onizawa
M
,
Nagaishi
T
,
Kanai
T
,
Nagano
K
,
Oshima
S
,
Nemoto
Y
, et al
.
Signaling pathway via TNF-alpha/NF-kappaB in intestinal epithelial cells may be directly involved in colitis-associated carcinogenesis
.
Am J Physiol Gastrointest Liver Physiol
2009
;
296
:
G850
9
.
48.
Matsumoto
S
,
Hara
T
,
Mitsuyama
K
,
Yamamoto
M
,
Tsuruta
O
,
Sata
M
, et al
.
Essential roles of IL-6 trans-signaling in colonic epithelial cells, induced by the IL-6/soluble-IL-6 receptor derived from lamina propria macrophages, on the development of colitis-associated premalignant cancer in a murine model
.
J Immunol
2010
;
184
:
1543
51
.
49.
Grivennikov
S
,
Karin
E
,
Terzic
J
,
Mucida
D
,
Yu
GY
,
Vallabhapurapu
S
, et al
.
IL-6 and Stat3 are required for survival of intestinal epithelial cells and development of colitis-associated cancer
.
Cancer Cell
2009
;
15
:
103
13
.
50.
Buchele
V
,
Konein
P
,
Vogler
T
,
Kunert
T
,
Enderle
K
,
Khan
H
, et al
.
Th17 cell-mediated colitis is positively regulated by interferon regulatory factor 4 in a T cell-extrinsic manner
.
Front Immunol
2020
;
11
:
590893
.
51.
Saleh
M
,
Trinchieri
G
.
Innate immune mechanisms of colitis and colitis-associated colorectal cancer
.
Nat Rev Immunol
2011
;
11
:
9
20
.
52.
Lagisetty
KH
,
McEwen
DP
,
Nancarrow
DJ
,
Schiebel
JG
,
Ferrer-Torres
D
,
Ray
D
, et al
.
Immune determinants of Barrett's progression to esophageal adenocarcinoma
.
JCI Insight
2021
;
6
:
e143888
.
53.
Lopez
A
,
Pouillon
L
,
Beaugerie
L
,
Danese
S
,
Peyrin-Biroulet
L
.
Colorectal cancer prevention in patients with ulcerative colitis
.
Best Pract Res Clin Gastroenterol
2018
;
32–33
:
103
9
.
54.
Peters
Y
,
Al-Kaabi
A
,
Shaheen
NJ
,
Chak
A
,
Blum
A
,
Souza
RF
, et al
.
Barrett oesophagus
.
Nat Rev Dis Primers
2019
;
5
:
35
.
55.
Duraturo
F
,
Liccardo
R
,
De Rosa
M
,
Izzo
P
.
Genetics, diagnosis and treatment of Lynch syndrome: old lessons and current challenges
.
Oncol Lett
2019
;
17
:
3048
54
.
56.
Kloor
M
,
von Knebel Doeberitz
M
.
The immune biology of microsatellite-unstable cancer
.
Trends Cancer
2016
;
2
:
121
33
.
57.
Chang
K
,
Taggart
MW
,
Reyes-Uribe
L
,
Borras
E
,
Riquelme
E
,
Barnett
RM
, et al
.
Immune profiling of premalignant lesions in patients with lynch syndrome
.
JAMA Oncol
2018
;
4
:
1085
92
.
58.
Reyes-Uribe
L
,
Wu
W
,
Gelincik
O
,
Bommi
PV
,
Francisco-Cruz
A
,
Solis
LM
, et al
.
Naproxen chemoprevention promotes immune activation in Lynch syndrome colorectal mucosa
.
Gut
2021
;
70
:
555
66
.
59.
Gebert
J
,
Gelincik
O
,
Oezcan-Wahlbrink
M
,
Marshall
JD
,
Hernandez-Sanchez
A
,
Urban
K
, et al
.
Recurrent frameshift neoantigen vaccine elicits protective immunity with reduced tumor burden and improved overall survival in a lynch syndrome mouse model
.
Gastroenterology
2021
;
161
:
1288
302
.
60.
Spencer
CN
,
McQuade
JL
,
Gopalakrishnan
V
,
McCulloch
JA
,
Vetizou
M
,
Cogdill
AP
, et al
.
Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response
.
Science
2021
;
374
:
1632
40
.
61.
Chen
ZF
,
Ai
LY
,
Wang
JL
,
Ren
LL
,
Yu
YN
,
Xu
J
, et al
.
Probiotics Clostridium butyricum and Bacillus subtilis ameliorate intestinal tumorigenesis
.
Future Microbiol
2015
;
10
:
1433
45
.
62.
Gamallat
Y
,
Meyiah
A
,
Kuugbee
ED
,
Hago
AM
,
Chiwala
G
,
Awadasseid
A
, et al
.
Lactobacillus rhamnosus induced epithelial cell apoptosis, ameliorates inflammation and prevents colon cancer development in an animal model
.
Biomed Pharmacother
2016
;
83
:
536
41
.
63.
Kuugbee
ED
,
Shang
X
,
Gamallat
Y
,
Bamba
D
,
Awadasseid
A
,
Suliman
MA
, et al
.
Structural change in microbiota by a probiotic cocktail enhances the gut barrier and reduces cancer via TLR2 signaling in a rat model of colon cancer
.
Dig Dis Sci
2016
;
61
:
2908
20
.
64.
Rafter
J
,
Bennett
M
,
Caderni
G
,
Clune
Y
,
Hughes
R
,
Karlsson
PC
, et al
.
Dietary synbiotics reduce cancer risk factors in polypectomized and colon cancer patients
.
Am J Clin Nutr
2007
;
85
:
488
96
.
65.
Ishikawa
H
,
Akedo
I
,
Otani
T
,
Suzuki
T
,
Nakamura
T
,
Takeyama
I
, et al
.
Randomized trial of dietary fiber and Lactobacillus casei administration for prevention of colorectal tumors
.
Int J Cancer
2005
;
116
:
762
7
.
66.
Zhang
X
,
Browman
G
,
Siu
W
,
Basen-Engquist
KM
,
Hanash
SM
,
Hoffman
KL
, et al
.
The BE GONE trial study protocol: a randomized crossover dietary intervention of dry beans targeting the gut microbiome of overweight and obese patients with a history of colorectal polyps or cancer
.
BMC Cancer
2019
;
19
:
1233
.
67.
Daniel
CR
,
Park
Y
,
Chow
WH
,
Graubard
BI
,
Hollenbeck
AR
,
Sinha
R
.
Intake of fiber and fiber-rich plant foods is associated with a lower risk of renal cell carcinoma in a large US cohort
.
Am J Clin Nutr
2013
;
97
:
1036
43
.
68.
Zhang
C
,
Monk
JM
,
Lu
JT
,
Zarepoor
L
,
Wu
W
,
Liu
R
, et al
.
Cooked navy and black bean diets improve biomarkers of colon health and reduce inflammation during colitis
.
Br J Nutr
2014
;
111
:
1549
63
.
69.
Baxter
BA
,
Oppel
RC
,
Ryan
EP
.
Navy beans impact the stool metabolome and metabolic pathways for colon health in cancer survivors
.
Nutrients
2018
;
11
:
28
.
70.
Sheflin
AM
,
Borresen
EC
,
Kirkwood
JS
,
Boot
CM
,
Whitney
AK
,
Lu
S
, et al
.
Dietary supplementation with rice bran or navy bean alters gut bacterial metabolism in colorectal cancer survivors
.
Mol Nutr Food Res
2017
;
61
:
10.1002/mnfr.201500905
.
71.
Serrano
MJ
,
Garrido-Navas
MC
,
Diaz Mochon
JJ
,
Cristofanilli
M
,
Gil-Bazo
I
,
Pauwels
P
, et al
.
Precision prevention and cancer interception: the new challenges of liquid biopsy
.
Cancer Discov
2020
;
10
:
1635
44
.
72.
Toy
R
,
Bauer
L
,
Hoimes
C
,
Ghaghada
KB
,
Karathanasis
E
.
Targeted nanotechnology for cancer imaging
.
Adv Drug Deliv Rev
2014
;
76
:
79
97
.
73.
Zhang
P
,
Zhou
X
,
He
M
,
Shang
Y
,
Tetlow
AL
,
Godwin
AK
, et al
.
Ultrasensitive detection of circulating exosomes with a 3D-nanopatterned microfluidic chip
.
Nat Biomed Eng
2019
;
3
:
438
51
.
74.
Miller
MS
,
Allen
PJ
,
Brown
PH
,
Chan
AT
,
Clapper
ML
,
Dashwood
RH
, et al
.
Meeting report: translational advances in cancer prevention agent development meeting
.
J Cancer Prev
2021
;
26
:
71
82
.
75.
Lam
KC
,
Araya
RE
,
Huang
A
,
Chen
Q
,
Di Modica
M
,
Rodrigues
RR
, et al
.
Microbiota triggers STING-type I IFN-dependent monocyte reprogramming of the tumor microenvironment
.
Cell
2021
;
184
:
5338
56
.
76.
Simpson
RC
,
Shanahan
ER
,
Batten
M
,
Reijers
ILM
,
Read
M
,
Silva
IP
, et al
.
Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome
.
Nat Med
2022
;
28
:
2344
52
.