Tumor Microbiome Research Articles

Abstract 1365: The spatially resolved host-microbiome sequencing platform reveals the interaction between bacteria and cancer stem cell microinches

Abstract The tumor microbiome is a unique element that appears differently for each type of cancer in a person. Currently, intratumoral host-microbiome sequencing was only done by bulk tissue analysis which means little is understood when it comes to the spatial distribution of microbiota in the heterogeneous tumor microenvironment and the localized effect of the microbiota. Breast cancer is known to be one of the cancers rich in the microbiome. We focused on cancer stem cell-like microniches related to the tumor microenvironment of triple-negative breast cancer(TNBC). We adapted SLACS(Spatially resolved Laser activated Cell Sorter) which isolates the region of interest from immunofluorescence-stained samples using a laser, providing the spatial distribution of localized microbiota in rare cancer stem cell samples. By applying SLACS to point out the breast cancer stem cell micro-niches, we discovered that more microbes flourished in ALDH1 high/CD44 high groups rather than normal cells. We also identified the composition of the microbiota was different in cancer stem cells depending on the degree of expression of the marker. Comparing RNA-seq data of host and microbiome sequencing with functional studies, we reveal the distribution of microbiota in breast tumors and interactions between cancer stem cells and microbiota. Collectively, we found the spatial pattern of the microbiota localized in cancer stem cell microniches and how cells and bacteria interact with each other more precisely. Citation Format: Gyeongjun Kim. The spatially resolved host-microbiome sequencing platform reveals the interaction between bacteria and cancer stem cell microinches [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1365.

Abstract 1216: Virome characterization in different types of non-Hodgkin lymphoma

Abstract Non-Hodgkin's lymphoma (NHL) is a heterogeneous group of lymphoid tissue neoplasms, with different clinical, genetic and morphological aspects. It is the most common form of hematological malignancy worldwide. In addition to risk factors, some infectious agents cause or are related to the risk of developing NHL. These include Epstein Barr virus (EBV), human herpes virus 8, human T-cell lymphotropic virus type 1, human immunodeficiency virus, hepatitis C virus, and the H. pylori. Overall, cancer attributable to infections accounted for 15.4% of new cases in 2012, and this number may increase due to improvements in molecular methodologies. Recently, other infectious agents have been associated with NHL, such as human pegivirus and cutavirus. Although factors related to immune function and the infectious agents described play a relevant role in the etiology of NHL, these factors do not explain most cases, suggesting that others factors or infectious agents could be involved in NHL development. Identifying possible pathogens associated with NHL and understanding the cancer-infectious agents relationship is essential for the development of prevention and screening aproaches. The aim of this study is to characterize the viral composition of the tumor microbiome in different types of NHL. Tumor tissue samples from NHL stored at the Brazilian National Cancer Institute were processed for viral DNA and RNA extraction. The viral nucleic acids were prepared for 19 samples with the Nextera XT kit and sequenced on an Illumina MiSeq platform. Virus identification analyses were performed by comparing the sequences obtained with viral sequences in the GenBank database through the BLASTX tool. Most samples were from diffuse large B cell lymphoma (DLBCL; n = 11), followed by marginal zone and follicular lymphoma (three cases each), and small lymphocytic and non-B, non-T cell lymphoma (one case each). A median of 46% of the obtained reads mapped to the human genome. Among the remaining reads, four viral families were identified: Anelloviridae, Flaviviridae, Herpesviridae and Papillomaviridae. EBV, a herpervirus associated with different types of NHL, was found in one gastric DLBCL. Anelloviridae reads included only the genus Alphatorquevirus and were found in five DLBCL. This virus family has a ubiquitous presence, without any clinical manifestation so far described in humans. However, anellovirus viral load has been associated with the subject’s immune status. Different human papillomaviruses from the Alpha, Beta and Gamma genera were found in six samples, comprising follicular lymphoma and DLBCL. The flavivirus human pegivirus was found in one DLBCL. Some recent studies associated this later virus with risk of lymphoma. In summary, this study describes the viral diversity found in NHL, showing the presence of viruses not yet associated with this neoplasia. Additional studies are warranted to clarify the role of these viruses in the etiology of NHL. Citation Format: Juliana D. Siqueira, Esmeralda A. Soares, Marcelo A. Soares. Virome characterization in different types of non-Hodgkin lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1216.

Abstract 5909: Characterization of the lung cancer microbiome using whole genome sequencing

Abstract Microbiome studies have been rapidly increasing over the last decade, providing valuable insights into the commensal bacterial contribution to human physiology and disease, including human cancer. Many studies have demonstrated the important roles of the microbiome in cancer progression, anti-tumor immunity, resistance to therapies, metastasis formation, and in some rare cases even cancer development through the production of genotoxins. However, relatively few studies have analyzed the lung cancer microbiome, and both its composition and role in cancer progression are largely unknown. To characterize the microbiome of tumor and matched normal lung tissues, we performed whole-genome sequencing (WGS) in 872 never smokers using the Kraken pipeline. At the phylum level, WGS analyses of tumor and normal samples showed predominantly Proteobacteria and Actinobacteria (58% and 32%, respectively). Notably, we found overall similar microbiome composition in tumor and normal lung tissue samples. At the genus level, Cutibacterium, Klebsiella, Pseudomonas, Sphingomonas, Staphylococcus, and Acinetobacter genera were among the most abundant bacteria in tumor and normal tissues, alike, and the genera Prevotella, Corynebacterium, and Streptococcus were more abundant in tumor samples compared to normal lung tissue. Comparison of alpha diversity at the genus level between tumors and normal samples showed no substantial difference. We are currently investigating whether the microbiome composition varies by lung tumor anatomical location, sex, histology, study subjects’ geographical location, and immune microenvironment. We will also investigate whether the tumor microbiome composition varies in relation to important genomic features, like cancer driver genes and mutational signatures. Finally, we have 16s rRNA seq data from 771 tumor and normal lung tissues from never smokers and we will compare bacterial microbiome composition and diversity based on WGS and 16s rRNA seq for the same samples. This study, based on the largest analysis of lung microbiome to date, is poised to provide important insights into the role of commensal microbiota in shaping lung tumor development and progression. Citation Format: John McElderry, Tongwu Zhang, Jianxin Shi, Maria Teresa Landi. Characterization of the lung cancer microbiome using whole genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5909.

PD25-08 THE BLADDER TUMOR MICROBIOME MAY AUGMENT RESPONSE TO BCG IN NON-MUSCLE INVASIVE BLADDER CANCER

You have accessJournal of UrologyCME1 Apr 2023PD25-08 THE BLADDER TUMOR MICROBIOME MAY AUGMENT RESPONSE TO BCG IN NON-MUSCLE INVASIVE BLADDER CANCER Zaeem Lone, Jacob Knorr, Glenn Werneburg, Ava Adler, Jose Agudelo, Rebecca Campbell, Petar Bajic, Nima Almassi, Christopher Weight, Georges Pascal-Haber, Aaron Miller, and Byron Lee Zaeem LoneZaeem Lone More articles by this author , Jacob KnorrJacob Knorr More articles by this author , Glenn WerneburgGlenn Werneburg More articles by this author , Ava AdlerAva Adler More articles by this author , Jose AgudeloJose Agudelo More articles by this author , Rebecca CampbellRebecca Campbell More articles by this author , Petar BajicPetar Bajic More articles by this author , Nima AlmassiNima Almassi More articles by this author , Christopher WeightChristopher Weight More articles by this author , Georges Pascal-HaberGeorges Pascal-Haber More articles by this author , Aaron MillerAaron Miller More articles by this author , and Byron LeeByron Lee More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003303.08AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Intravesical installation of BCG has been the gold standard for the management of non-muscle invasive bladder cancer (NMIBC). However, approximately 30-40% of patients experience treatment failure and it remains unclear who will benefit from this therapy. One potential modifiable factor in treatment response may be the urinary microbiome. Therefore, we sought to investigate how the urinary microbiome may differ between BCG responders and non-responders and identify any commensal bacteria that might increase the efficacy of this therapy. METHODS: 16S next-generation sequencing (NGS) and shotgun metagenomics were performed on formalin-fixed bladder tumors from patients prior to intravesical BCG therapy for NMIBC. BCG responders was defined as no recurrence two years after induction. Differences in the alpha and beta diversity of the two populations were compared. Subsequently, to validate the NGS data, GFP-tagged BCG was co-cultured with a urothelial carcinoma (UC) cell line (SW780) and candidate bacteria based on the NGS data. A Pearson-Chi Square test was utilized to compare percent internalization. Additionally, fresh tumor samples were collected at the time of transurethral resection of bladder tumor (TURBT) and were cultured in five different media conditions to confirm the viability of the tumor microbiome and quantify the bacterial mass per sample. RESULTS: Forty-seven patients (23 responders, 24 non-responders) were included in the analysis. Overall microbiome composition differed significantly as determined by both NGS (p=0.042) and shotgun metagenomics (p=0.047). Lactobacillus spp were significantly enriched in the BCG responders. Co-culture with increasing concentrations of Lactobacillus crispatus resulted in increased BCG-GFP internalization in UCC (179/1133, 16%) when compared to controls (75/1166, 6%) (p<0.001). Additionally, from ten fresh tumor samples, four samples produced viable bacteria through culture-based approaches and we calculated tumor bacterial density at 1.25×106 colony forming units/gram of tissue. CONCLUSIONS: A compositional difference exists in the tumor microbiome of BCG responders and non-responders. Lactobacillus crispatus was associated with a significant increase in the internalization of BCG. Our findings suggest that an association exists between the tumor microbiome and response to BCG, which may offer new strategies to improve intravesical therapy for NMIBC patients. Source of Funding: Case Comprehensive Cancer Center Summer Medical Student Award © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e732 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Zaeem Lone More articles by this author Jacob Knorr More articles by this author Glenn Werneburg More articles by this author Ava Adler More articles by this author Jose Agudelo More articles by this author Rebecca Campbell More articles by this author Petar Bajic More articles by this author Nima Almassi More articles by this author Christopher Weight More articles by this author Georges Pascal-Haber More articles by this author Aaron Miller More articles by this author Byron Lee More articles by this author Expand All Advertisement PDF downloadLoading ...

Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data.

Sequencing-based approaches for the analysis of microbial communities are susceptible to contamination, which could mask biological signals or generate artifactual ones. Methods for in silico decontamination using controls are routinely used, but do not make optimal use of information shared across samples and cannot handle taxa that only partially originate in contamination or leakage of biological material into controls. Here we present Source tracking for Contamination Removal in microBiomes (SCRuB), a probabilistic in silico decontamination method that incorporates shared information across multiple samples and controls to precisely identify and remove contamination. We validate the accuracy of SCRuB in multiple data-driven simulations and experiments, including induced contamination, and demonstrate that it outperforms state-of-the-art methods by an average of 15-20 times. We showcase the robustness of SCRuB across multiple ecosystems, data types and sequencing depths. Demonstrating its applicability to microbiome research, SCRuB facilitates improved predictions of host phenotypes, most notably the prediction of treatment response in melanoma patients using decontaminated tumor microbiome data.

Vaginal and tumor microbiomes in gynecological cancer (Review).

Cervical, ovarian and endometrial cancer are the three most common types of gynecologic cancer. As a hub, the vagina connects the site of gynecological cancer with the external environment. Lactobacilli participate in the formation of a healthy vaginal microenvironment as the first line of defense against pathogen invasion; a dysbiotic vaginal microenvironment loses its original protective function and is associated with the onset, metastasis, poor efficacy and poor prognosis of gynecological cancer. The early diagnosis of cancer is the key to improve the survival time of patients with cancer. The screening of Porphyromonas, Sneathia and Atopobium vaginae, and other microbial markers, can assist the diagnosis of gynecological cancer, and screen out the high-risk population as early as possible. With the in-depth study of the microbes in tumor tissues, reasearchers have analyzed the immunological associations of microorganisms in tumor tissues. Due to the structural-functional interconnection between the organ of gynecological tumorigenesis and the vagina, the present study aims to review the relationship between vaginal and tumor microorganisms and gynecological cancer in terms of occurrence, screening, treatment and prognosis.

The colorectal cancer-specific microbiome regulation and immune response activation via an artificial biomimetic nanovaccine

The tumor microbiome has been reported to be composed of tumor-type-specific intracellular bacteria and is closely related to tumor progression and the response to anticancer therapies. Although antitumor treatments focusing on the abnormal tumor microenvironment (TME), such as anti-bacterial or TME regulatory approaches, have been shown to significantly improve antitumor efficacy, strategies that can interfere with the microbial environment to inhibit tumor growth and activate immune response are rare. Here, we have constructed an artificially modified biomimetic nanovaccine PMO for the first time using an inactivated anaerobic bacterium P. anaerobius, a colorectal cancer (CRC)-specific bacterium carrying therapeutical agents to regulate the microbial environment. The PMO could sneak into tumors due to its natural affinity to CRC, which has a particularly rich and diverse microbiome that results in therapy resistance. The PMO could not only achieve significant tumor growth suppression by precisely delivering therapeutical MnO2 and OXA to CRC tissues but also effectively prevent tumor recurrence by the cascade reaction of activating the tumor immune responses after reshaping the microbial environment. This nanovaccine has provided the tremendous clinical potential for designing new treatment strategies for drug-resistant tumors from the perspective of microbial environmental regulation and improving the prognosis of patients.

Sparse tree-based clustering of microbiome data to characterize microbiome heterogeneity in pancreatic cancer.

There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with similar microbiome profiles. We propose a novel unsupervised clustering approach in the Bayesian framework that innovates over existing model-based clustering approaches, such as the Dirichlet multinomial mixture model, in three key respects: we incorporate feature selection, learn the appropriate number of clusters from the data, and integrate information on the tree structure relating the observed features. We compare the performance of our proposed method to existing methods on simulated data designed to mimic real microbiome data. We then illustrate results obtained for our motivating data set, a clinical study aimed at characterizing the tumor microbiome of pancreatic cancer patients.

Colon Cancer Microbiome Landscaping: Differences in Right- and Left-Sided Colon Cancer and a Tumor Microbiome-Ileal Microbiome Association.

In the current era of precision oncology, it is widely acknowledged that CRC is a heterogeneous disease entity. Tumor location (right- or left-sided colon cancer or rectal cancer) is a crucial factor in determining disease progression as well as prognosis and influences disease management. In the last decade, numerous works have reported that the microbiome is an important element of CRC carcinogenesis, progression and therapy response. Owing to the heterogeneous nature of microbiomes, the findings of these studies were inconsistent. The majority of the studies combined colon cancer (CC) and rectal cancer (RC) samples as CRC for analysis. Furthermore, the small intestine, as the major site for immune surveillance in the gut, is understudied compared to the colon. Thus, the CRC heterogeneity puzzle is far from being solved, and more research is necessary for prospective trials that separately investigate CC and RC. Our prospective study aimed to map the colon cancer landscape using 16S rRNA amplicon sequencing in biopsy samples from the terminal ileum, healthy colon tissue, healthy rectal tissue and tumor tissue as well as in preoperative and postoperative stool samples of 41 patients. While fecal samples provide a good approximation of the average gut microbiome composition, mucosal biopsies allow for detecting subtle variations in local microbial communities. In particular, the small bowel microbiome has remained poorly characterized, mainly because of sampling difficulties. Our analysis revealed the following: (i) right- and left-sided colon cancers harbor distinct and diverse microbiomes, (ii) the tumor microbiome leads to a more consistent cancer-defined microbiome between locations and reveals a tumor microbiome-ileal microbiome association, (iii) the stool only partly reflects the microbiome landscape in patients with CC, and (iv) mechanical bowel preparation and perioperative antibiotics together with surgery result in major changes in the stool microbiome, characterized by a significant increase in the abundance of potentially pathogenic bacteria, such as Enterococcus. Collectively, our results provide new and valuable insights into the complex microbiome landscape in patients with colon cancer.

Microbiome and spatially resolved metabolomics analysis reveal the anticancer role of gut Akkermansia muciniphila by crosstalk with intratumoral microbiota and reprogramming tumoral metabolism in mice

ABSTRACT Although gut microbiota has been linked to cancer, little is known about the crosstalk between gut- and intratumoral-microbiomes. The goal of this study was to determine whether gut Akkermansia muciniphila (Akk) is involved in the regulation of intratumoral microbiome and metabolic contexture, leading to an anticancer effect on lung cancer. We evaluated the effects of gut endogenous or gavaged exogenous Akk on the tumorigenesis using the Lewis lung cancer mouse model. Feces, blood, and tumor tissue samples were collected for 16S rDNA sequencing. We then conducted spatially resolved metabolomics profiling to discover cancer metabolites in situ directly and to characterize the overall Akk-regulated metabolic features, followed by the correlation analysis of intratumoral bacteria with metabolic network. Our results showed that both endogenous and exogenous gavaged Akk significantly inhibited tumorigenesis. Moreover, we detected increased Akk abundance in blood circulation or tumor tissue by 16S rDNA sequencing in the Akk gavaged mice, compared with the control mice. Of great interest, gavaged Akk may migrate into tumor tissue and influence the composition of intratumoral microbiome. Spatially resolved metabolomics analysis revealed that the gut-derived Akk was able to regulate tumor metabolic pathways, from metabolites to enzymes. Finally, our study identified a significant correlation between the gut Akk-regulated intratumoral bacteria and metabolic network. Together, gut-derived Akk may migrate into blood circulation, and subsequently colonize into lung cancer tissue, which contributes to the suppression of tumorigenesis by influencing tumoral symbiotic microbiome and reprogramming tumoral metabolism, although more studies are needed.

Racial disparities in tumor microbiome in young-onset and average-onset colorectal cancer.

13 Background: The occurrence of young-onset colorectal cancer (yoCRC) is rising alarmingly, with a disproportionate incidence in Black patients as compared to White. We and others have previously shown differences in tumor microbiomes between yoCRC and average-onset colorectal cancer (aoCRC), but it is unknown if these differences contribute to racial disparities. We therefore analyzed racial differences in the intra-tumoral microbiome of CRC in young adults (&lt;50 years). Methods: We analyzed 277 samples of histologically confirmed cases of stage I-IV CRC patients identified as either non-Hispanic Black or non-Hispanic White, who underwent surgical resection at Cleveland Clinic from year 2000-2020, who consented to a prospective biorepository. Fresh frozen specimens from the primary tumor with paired adjacent nonmalignant tissue were analyzed. The 16s rRNA gene was amplified and sequenced using V4 region primers and Illumina’s MiSeq system. Using DADA2, the quality filtered 16S rRNA amplicon reads were clustered and annotated as amplicon sequence variants (ASVs). The abundance count matrix was analyzed for alpha and beta diversity and differential abundance analysis (DAA) using Phyloseq package. Statistical tests included analysis of variance (ANOVA), permutational multivariate analysis (PERMANOVA), linear regression and Wilcoxon test. DAA and correlation analysis were controlled for false discovery rate using Benjamini Hochberg correction. Results: Differential abundance analysis highlighted key differences in the microbiome composition of Black and White patients with yoCRC. Amongst Black patients, the most prevalent taxa were Limosilactobacillus, Bacillus, Staphylococcus, Listeria and Akkermansia, whereas amongst White patients the most prevalent taxa were Enterococcus and Escherichia-Shigella (Table). Microbial profiles were also significantly different between Black patients with yoCRC and aoCRC and between White patients with yoCRC and aoCRC. At ASV level, the microbiome of Black yoCRC is more similar (R2 =0.87) to Black aoCRC, in comparison to white yoCRC (R2=0.57). Conclusions: We found significant differences between the intra-tumoral microbiome of yoCRC in the United States by race. Future epidemiologic studies and public health interventions need to account for these differences to reduce risk of yoCRC across various US populations. [Table: see text]

Prospective characterization of oral and gut microbiome in a high-risk pancreatic cancer cohort.

691 Background: Pancreatic cancer (PC) is the third leading cause of cancer death in the United States. The high mortality associated with PC is attributed to multiple reasons: lack of effective therapies, aggressive biology and late diagnosis. Due to the absence of reliable early disease biomarkers, PC screening is largely dependent on imaging. Recent studies have highlighted the importance of the gut and tumor microbiome in PC. We present here the first report of oral and gut microbiome prospective analysis of PC high-risk individuals (PC-HRI) undergoing screening. Methods: We collected periodontal and stool samples at the University of Texas MD Anderson Cancer Center from 2017-2022. A total of 448 samples, consisting of 250 oral and 198 gut samples were obtained. Samples were collected from PC (n=73), PC-HRI (n=34), and healthy (n=143) individuals. 16s rRNA sequencing was used to characterize the oral and gut microbiome and statistical analysis and correlation with imaging and clinical characteristics were performed. Results: We identified three phyla, namely Proteobacteria, Actinobacteria, and Fusobacteria as significantly more abundant in the gut microbiome of PC patients. Conversely, Proteobacteria was decreased in the oral microbiome of PC patients. At the class level, Gammaproteobacteria (GP) oral/gut ratio was significantly decreased in PC patients compared with healthy individuals (p=0.02). Analysis of PC-HRI revealed also low GP oral/gut ratio in high-risk individuals who were diagnosed with worrisome pancreatic focal lesions. Interestingly, Gammaproteobacteria (GP) is one of the main classes of bacteria detected in pancreatic cancer tissue. GP shifts in oral and gut environments could be implicated in pancreatic early tumorigenesis and serve as biomarker of the disease. Additionally, gut bacteria with metabolic pathways related to lipid metabolism were more enriched in PC patients and PC-HRI with focal lesions compared to healthy controls. Conclusions: Gammaproteobacteria oral/gut ratio represents a potential novel biomarker which could predict presence of early high risk-pancreatic focal lesions in PC-HRI. Taken together, this report provides observational evidence about changes in oral and gut microbiome in patients with pancreatic cancer but even more importantly, the fact that those changes could be detected in PC-HRI with early high-risk lesions. Broader validation in other high-risk cohorts would be required. Detection of GP oral/gut ratio would represent an inexpensive, non-invasive method that could be useful for PC screening. Functional studies should be performed to determine how GP shifts can contribute with pancreatic tumorigenesis. Research supported by CPRIT (Grant Number: RP200173) and philanthropic funding through the MD Anderson Moonshot Program.

A pilot study of gut microbiome modulation to enable efficacy of neoadjuvant checkpoint-based immunotherapy (IO) following chemotherapy in pancreatic ductal adenocarcinoma (PDAC).

TPS759 Background: Neoadjuvant therapy is now a standard strategy for localized PDAC, and this preoperative window provides an excellent opportunity in which to test novel therapeutic approaches. Trials using IO in PDAC have largely been unsuccessful, and immune tolerance is implicated as a major mechanism of IO resistance. The gut and tumor microbiome have emerged as key modulators of response to both IO and chemotherapy. High tumor microbial diversity has been linked to longer survival in PDAC, and gut microbiota may have the ability to colonize pancreatic tumors. There is preclinical evidence that endogenous microbiota promotes the immunosuppressive tumor microenvironment characteristic of PDAC through stimulation of pro-tumor regulatory T cells and myeloid-derived suppressor cells at the expense of anti-tumor activated CD4+ and CD8+ T cells. Further, preclinical data show that ablation of the gut microbiota may induce T cell activation, improve immune surveillance, and increase sensitivity to IO. We hypothesize that ablative antibiotics (abx) will activate tumor infiltrating T cells and enhance IO activity in PDAC. Methods: This is a multi-center, single-arm, open-label pilot study of pre-operative chemotherapy followed by abx and pembrolizumab to evaluate overall immune response to abx + IO. Eligible patients will have histologically confirmed, resectable PDAC, without probiotic consumption or use of immunosuppressive agents. Patients will be enrolled at diagnosis after undergoing a baseline biopsy. They will then receive mFOLFIRINOX every 2 weeks for 5 cycles. After completion of chemotherapy, ciprofloxacin 500 mg PO BID and metronidazole 500 mg PO TID will be administered for 21 days, and pembrolizumab 200 mg IV x1 will be given 7 days after initiation of abx. Patients will then undergo surgical resection and adjuvant therapy at the investigators’ discretion. On-treatment biopsy will be obtained prior to cycle 5 of mFOLFIRINOX. Blood and stool will be collected at baseline, during mFOLFIRINOX therapy, before and after pembrolizumab administration, and postoperatively. The primary endpoint is the overall immune response, which will be measured as activation of one or more of the T cell markers HLA-DR, CD38, CD25, Ki67, and CD69, defined as an increase in expression level of at least 20% from the on-treatment specimen to the surgical specimen, before and after abx + IO. Key secondary endpoints will be the evaluation of adverse events, R0 resection rate, histologic regression score, objective response rate, and overall survival rate. Correlative studies will be carried out to evaluate immune and microbiome changes in the blood and tissue following abx and pembrolizumab. These findings will be correlated with clinical endpoints. The target study accrual is 25 patients. Clinical trial information: NCT05462496 .

A New Treatment Landscape for RCC: Association of the Human Microbiome with Improved Outcomes in RCC.

Microbes play different roles in metabolism, local or systemic inflammation, and immunity, and the human microbiome in tumor microenvironment (TME) is important for modulating the response to immunotherapy in cancer patients. Renal cell carcinoma (RCC) is an immunogenic tumor, and immunotherapy is the backbone of its treatment. Correlations between the microbiome and responsiveness to immune checkpoint inhibitors have been reported. This review summarizes the recent therapeutic strategies for RCC and the effects of TME on the systemic therapy of RCC. The current understanding and advances in microbiome research and the relationship between the microbiome and the response to immunotherapy for RCC are also discussed. Improving our understanding of the role of the microbiome in RCC treatment will facilitate the development of microbiome targeting therapies to modify the tumor microbiome and improve treatment outcomes.

Caulobacter and Novosphingobium in tumor tissues are associated with colorectal cancer outcomes.

Diversity and composition of the gut microbiome are associated with cancer patient outcomes including colorectal cancer (CRC). A growing number of evidence indicates that Fusobacterium nucleatum (Fn) in CRC tissue is associated with worse survival. However, few studies have further analyzed the differences in bacteria in tumor tissues of different patients depending on the survival time of CRC patients. Therefore, there is a need to further explore the bacterial differences in tumor tissues of patients with different prognoses and to identify key bacteria for analysis. Here, we sought to compare the differences in tumor microbiome between patients with long-term survival (LS) longer than 3 years or 4 and 5 years and patients with short-term survival (SS) in the present study cohort. We found that there were significant differences in tumor microbiome between the LS and SS and two bacteria-Caulobacter and Novosphingobium-that are present in all of the three groups. Furthermore, by analyzing bacteria in different clinical features, we also found that lower levels of microbiome (Caulobacter and Novosphingobium) have long-term survival and modulating microbiome in tumor tissue may provide an alternative way to predict the prognosis of CRC patients.

Monitoring and Modulating Diet and Gut Microbes to Enhance Response and Reduce Toxicity to Cancer Treatment.

The gut microbiome comprises a diverse array of microbial species that have been shown to dynamically modulate host immunity both locally and systemically, as well as contribute to tumorigenesis. In this review, we discuss the scientific evidence on the role that gut microbes and diet play in response and toxicity to cancer treatment. We highlight studies across multiple cancer cohorts that have shown an association between particular gut microbiome signatures and an improved response to immune checkpoint blockade, chemotherapy, and adoptive cell therapies, as well as the role of particular microbes in driving treatment-related toxicity and how the microbiome can be modulated through strategies, such as fecal transplant. We also summarize the current literature that implicate high fiber and ketogenic diets in improved response rates to immunotherapy and chemotherapy, respectively. Finally, we discuss the relevance of these findings in the context of patient care, advocate for a holistic approach to cancer treatment, and comment on the next frontier of targeted gut and tumor microbiome modulation through novel therapeutics, dietary intervention, and precision-medicine approaches.

Applying multi-omics toward tumor microbiome research.

Rather than a "short-term tenant," the tumor microbiome has been shown to play a vital role as a "permanent resident," affecting carcinogenesis, cancer development, metastasis, and cancer therapies. As the tumor microbiome has great potential to become a target for the early diagnosis and treatment of cancer, recent research on the relevance of the tumor microbiota has attracted a wide range of attention from various scientific fields, resulting in remarkable progress that benefits from the development of interdisciplinary technologies. However, there are still a great variety of challenges in this emerging area, such as the low biomass of intratumoral bacteria and unculturable character of some microbial species. Due to the complexity of tumor microbiome research (e.g., the heterogeneity of tumor microenvironment), new methods with high spatial and temporal resolution are urgently needed. Among these developing methods, multi-omics technologies (combinations of genomics, transcriptomics, proteomics, and metabolomics) are powerful approaches that can facilitate the understanding of the tumor microbiome on different levels of the central dogma. Therefore, multi-omics (especially single-cell omics) will make enormous impacts on the future studies of the interplay between microbes and tumor microenvironment. In this review, we have systematically summarized the advances in multi-omics and their existing and potential applications in tumor microbiome research, thus providing an omics toolbox for investigators to reference in the future.

The significant clinical correlation of the intratumor oral microbiome in oral squamous cell carcinoma based on tissue-derived sequencing.

Background: The microbiota is a critical component of the complex human microenvironment, impacting various physiological processes and disease development via the microbe-host interaction. In particular, the oral microbiota profoundly affects tumor development and progression. There is increasing evidence that oral microbiota is associated with the development of oral cancer, especially oral squamous cell carcinoma (OSCC). Methods: We comprehensively analyzed the oral microbiota in 133 OSCC samples worldwide. Subsequently, we evaluated the microbial compositions between OSCC patients and healthy people and their correlation with clinical parameters. The value of the oral microbiota as a diagnostic and prognostic biomarker was also determined. Results: This study found differences in critical oral microbiota between OSCC and normal controls. The most notable differences are present in p_Firmicutes, p_Actinobacteria, c_Fusobacteriia, o_Fusobacteriales, f_Fusobacteriaceae, and g_Fusobacterium. All six-level oral microorganisms were also associated with the clinical characteristics of OSCC, particularly with the clinical outcomes (survival time and status). We developed a predictive model based on this. We found that five different oral microorganisms have high confidence and can be used for clinical diagnosis and prognostic prediction, except for p_Actinobacteria. Conclusion: This study revealed that the intratumor oral microbiota of OSCC patients worldwide and the microbial signatures of OSCC patients possess similar properties in different regions, further refining the shortcomings of the current research field. We revealed that the oral microbiota could be used as a biomarker to reflect human health and disease progression status. This will provide new directions for tumor microbiome research. This means we can develop strategies through diet, probiotics, and antibiotics for cancer prevention and treatment.

Sorting Transcriptomics Immune Information from Tumor Molecular Features Allows Prediction of Response to Anti-PD1 Therapy in Patients with Advanced Melanoma.

Immunotherapy based on anti-PD1 antibodies has improved the outcome of advanced melanoma. However, prediction of response to immunotherapy remains an unmet need in the field. Tumor PD-L1 expression, mutational burden, gene profiles and microbiome profiles have been proposed as potential markers but are not used in clinical practice. Probabilistic graphical models and classificatory algorithms were used to classify melanoma tumor samples from a TCGA cohort. A cohort of patients with advanced melanoma treated with PD-1 inhibitors was also analyzed. We established that gene expression data can be grouped in two different layers of information: immune and molecular. In the TCGA, the molecular classification provided information on processes such as epidermis development and keratinization, melanogenesis, and extracellular space and membrane. The immune layer classification was able to distinguish between responders and non-responders to immunotherapy in an independent series of patients with advanced melanoma treated with PD-1 inhibitors. We established that the immune information is independent than molecular features of the tumors in melanoma TCGA cohort, and an immune classification of these tumors was established. This immune classification was capable to determine what patients are going to respond to immunotherapy in a new cohort of patients with advanced melanoma treated with PD-1 inhibitors Therefore, this immune signature could be useful to the clinicians to identify those patients who will respond to immunotherapy.

Functional Assay for Measuring Bacterial Degradation of Gemcitabine Chemotherapy.

Drug biotransformation by the host microbiome can impact the therapeutic success of treatment. In the context of cancer, drug degradation can take place within the microenvironment of the targeted tumor by intratumor bacteria. In pancreatic cancer, increased chemo-resistance against the frontline chemotherapy gemcitabine is thought to arise from drug degradation by the tumor microbiome. This bacterial-drug interaction highlights the need for developing rapid assays for monitoring bacterial gemcitabine breakdown. While chemical approaches such as high-performance liquid chromatography are suitable for this task, they require specialized equipment and expertise and are limited in throughput. Functional cell-based assays represent an alternate approach for performing this task. We developed a functional assay to monitor the rate of bacterial gemcitabine breakdown using a highly sensitive bacterial reporter strain. Our method relies on standard laboratory equipment and can be implemented at high throughput to monitor drug breakdown by hundreds of strains simultaneously. This functional assay can be readily adapted to monitor degradation of other drugs. Key features Quantification of gemcitabine breakdown by incubating bacteria that degrades the drug and subsequently testing the growth of a reporter strain on filtered supernatant. Use of an optimized reporter strain that was genetically engineered to be a non-degrader strain and highly sensitive to gemcitabine. A high-throughput assay performed in microplates that can be adjusted for identifying bacteria with a fast or slow gemcitabine degradation rate. The assay results can be compared to results from a standard curve with known drug concentrations to quantify degradation rate.