Abstract 3057: Characterization and functional analysis of microbiome in bladder cancer

Background: The role of microbiome in genitourinary cancer is an emerging field, with evidence implicating the important role of microbiome as causative factors or cofactors in tumorigenesis and drug metabolism. Our study aims to characterize healthy and bladder cancer enterotypes in the gut and identify functional alterations through the use of metagenomics data.

Methods: After prospective collection of 29 rectal swab samples of bladder cancer (BCa) patients undergoing cystectomy, and 32 healthy volunteers, we perform 16S rRNA amplicon sequencing on 61 samples (29 with bladder cancer, 32 without cancer). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to infer functional categories associated with taxonomic composition. The p values were adjusted using the false discovery rate. The a- and b-diversity analyses were performed using QIIME. The Mann- Whitney U test was employed to evaluate the statistical significance of b-diversity distances within and between groups of interest.

Results: Across all the bladder cancer stool samples, estimation of relative abundance revealed of the five most dominant bacterial populations was Bacteroidales ( 46.21%), Clostridiales ( 32.29%), Burkholderiales (9.07%), Erysipelotrichales (3.20%) and Lactobacillales ( 2.20%). In contrast, healthy controls exhibited an increased relative abundance of Enterobacteriales ( 10.75% vs 0.52%) and Pseudomonadales (8.33% vs 0.18%) as compared to tumor samples. The microbial diversity differences between Bca and normal samples showed no differences across alpha diversity metrics (Shannon diversity p > 0.05) as compared to normal tissue. However, there was significant difference in clustering of organisms as determined by principal coordinate analysis ( PCoA) ordination of unweighted UniFrac Distances, (p = 0.002). Furthermore, upon stratification of patients on smoking status (all healthy = nonsmokers), clustering persisted, albeit non smokers with bladder cancer displayed an intermediate across PCoA. Bca samples exhibited higher LDA score Campylobacterales (log change 8.0, p < 0.001, padj < 0.001), Fusobacteriales (log change 6.11, p < 0.001/padj< 0.01), Epysipelotrichales (log 2.55, p < 0.001/padj < 0.001), Actinomycetales (log change 1.86, p = 0.001/padj< 0.001), Verrucomicrobiales (log change 1.78, p = 0.017/padj= 0.031) and Enterobacteriales (log change -1.54,p = 0.017/padj= 0.132).

Conclusions: Our study provides preliminary evidence that the GI microbiota is different in bladder cancer patients. Collectively, our study highlights distinct microbial overexpression of Campylobacter and Fusobacterium in Bca cohort not previously reported, both implicated in tumorigenesis, and could serve as a target that could be modulated to enhance treatment response.

Citation Format: Laura Bukavina, Rashida Ginwala, Adam C. Calaway, Ilaha Isali, Megan Prunty, Mohit Sindhani, Lee Ponsky, Sarah Markt, Phillip Abbosh. Characterization and functional analysis of microbiome in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3057.

Gene network profiling in muscle-invasive bladder cancer: A systematic review and meta-analysis

BACKGROUND

Determining meta-analysis of transcriptional profiling of muscle-invasive bladder cancer (MIBC) through Gene Expression Omnibus (GEO) datasets has not been investigated. This study aims to define gene expression profiles in MIBC and to identify potential candidate genes and pathways.

OBJECTIVES

To review and evaluate gene expression studies in MIBC through publicly available RNA sequencing (RNA-Seq) and microarray data in order to identify potential prognostic and therapeutic targets for MIBC.

METHODS

A systematic literature search of the Ovid MEDLINE, PubMed, and Wiley Cochrane Central Register of Controlled Trials databases was performed using the terms "gene," "gene expression," and "bladder cancer" January 1, 1990 through March 2021 focused on populations with MIBC.

RESULTS

In the final analysis, GEO datasets were included. Fixed effect model was employed in the meta-analysis. Gene networking connections and gene-set functional analyses of the identified genes as differentially expressed in MIBC were performed using ImaGEO and GeneMANIA software. A heatmap for the upregulated and downregulated genes was generated along with the correlated pathways.

CONCLUSION

A total of 9 genes were reported in this analysis. Six genes were reported as upregulated (ProTα, SPINT1, UBE2E1, RAB25, KPNB1, HDAC1) and 3 genes as downregulated (NUP188, IPO13, NUP124). Genes were found to be involved in "ubiquitin mediated proteolysis," "protein processing in endoplasmic reticulum," "transcriptional misregulation in cancer," and "RNA transport" pathways.

Characterization of fungal mycobiome in bladder cancer

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Background: Bacterial dysbiosis accompanies carcinogenesis in malignancies such as colon, breast and pancreatic cancer. However, the role of fungal mycobiome has not been evaluated in bladder cancer. With the sexual dimorphism that exists within bladder cancer (Bca) prevalence and survival, our study aims to characterize fungal mycobiome composition in Bca. Methods: This is a single site, non-randomized, prospective study of patients with the diagnosis of muscle invasive bladder cancer (MIBC) undergoing cystectomy from September 2020 to May 2021. Stool samples were collected during surgery using aseptic technique. We utilized the ITS1 region from DNA sample extracts, which was amplified in triplicate using primers with high specificity for ascomycete fungi (fluorescently-labeled forward primer ITS1F (CTTGGTCATTTAGAGGAAGTAA) and unlabeled reverse primer ITS2 (GCTGCGTTCTTCATCGATGC). Fungal PCR products were separated on the SCE 9610 capillary DNA sequencer (Spectrumedix LLC, State College, PA) using GenoSpectrum software to convert fluorescent output into electropherograms. Hierarchical clustering by Bray-Curtis distance was performed using hclust2. Mean normalized abundance for each amplicon was calculated from the three PCR replicates of each sample, excluding means below 1%. Results: A total of 29 patients (17 males and 12 females) were enrolled. The median (IQR) age was 74 yo (63-77), males, and 68.5 yo (58-78), females. Per figure 1, Saccharomycecales dominated the fungal community at order level with mean relative abundance of 36.35% females, and 21.20%, males. (Figure 1D) Tremellales was the second most notable order, composing 8.22% and 5.13% of male and female samples. There were no differences seen in alpha and beta diversity (Figure 1C) (Figure 1A, C), notable differences were seen across orders. The greatest difference between sexes in LDA( M:F) were noted in Saccharomycecales (log change -4.686, p=0.001/ padj= 0.01), Tremellales (log change 5.119, p=0.001/padj= 0.01), and Sporidiobolales (log change 4.839, p=0.001 padj= 0.03). (Figure 1B). Female bladder cancer patients demonstrating an increase abundance of Saccharomycecale. When assessing differences in fungal composition in patients with history of neoadjuvant therapy( NAC) (receipt vs none), patients with history of NAC exhibited a 3.48 increase in Saccharomycecale (padj= 0.015 ), 4.81 increase Tremalles (padj= 0.009) and 4.37 increase Pleosporales(padj= 0.009) . Conclusions: Mycobiome is an integral part of gut microbiota, with fungal elements relatively poorly studied. Nevertheless, the association between fungal dysbiosis and carcinogenesis across multiple cancers exists. Our study is the first to characterize fungal profile in bladder cancer patients, stratified by sex and receipt of NAC, with results highlighting key fungal players: Saccharomycecale, Tremallales, Pleosoporales.

Characterization and functional analysis of microbiome in bladder cancer

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Background: The role of microbiome in genitourinary cancer is an emerging field, with evidence implicating the important role of microbiome as causative factors or cofactors in tumorigenesis and drug metabolism. Our study aims to characterize healthy and bladder cancer enterotypes in the gut and identify functional alterations through the use of metagenomics data. Methods: After prospective collection of 29 rectal swab samples of bladder cancer (BCa) patients undergoing cystectomy, and 32 healthy volunteers, we perform 16S rRNA amplicon sequencing on 61 samples (29 with bladder cancer, 32 without cancer). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to infer functional categories associated with taxonomic composition. The p values were adjusted using the false discovery rate. The a- and b-diversity analyses were performed using QIIME. The Mann-Whitney U test was employed to evaluate the statistical significance of b-diversity distances within and between groups of interest. Results: Across all the bladder cancer stool samples, estimation of relative abundance revealed of the five most dominant bacterial populations was Bacteroidales ( 46.21%), Clostridiales ( 32.29%), Burkholderiales (9.07%), Erysipelotrichales (3.20%) and Lactobacillales ( 2.20%). In contrast, healthy controls exhibited an increased relative abundance of Enterobacteriales ( 10.75% vs 0.52%) and Pseudomonadales (8.33% vs 0.18%) as compared to tumor samples. The microbial diversity differences between Bca and normal samples showed no differences across alpha diversity metrics (Shannon diversity p>0.05) as compared to normal tissue. However, there was significant difference in clustering of organisms as determined by principal coordinate analysis ( PCoA) ordination of unweighted UniFrac Distances, (p=0.002). Furthermore, upon stratification of patients on smoking status (all healthy=nonsmokers), clustering persisted, albeit non smokers with bladder cancer displayed an intermediate across PCoA. Bca samples exhibited higher LDA score Campylobacterales (log change 8.0, p<0.001, padj <0.001) ,Fusobacteriales (log change 6.11, p<0.001/ padj<0.01), Epysipelotrichales (log 2.55, p<0.001/ padj <0.001 ), Actinomycetales (log change 1.86, p=0.001/ padj<0.001), Verrucomicrobiales (log change 1.78, p=0.017/padj=0.031) and Enterobacteriales (log change -1.54,p=0.017/ padj= 0.132). Conclusions: In conclusion, our study provides preliminary evidence that the GI microbiota is different in bladder cancer patients. Collectively, our study highlights distinct microbial overexpression of Campylobacter and Fusobacterium in Bca cohort not previously reported, both implicated in tumorigenesis, and could serve as a target that could be modulated to enhance treatment response.

Mutations in renal cell carcinoma

Renal cell carcinoma (RCC) is a commonly diagnosed and histologically diverse urologic malignancy. Clear cell RCC (ccRCC) is by far the most common, followed by the papillary and chromophobe subtypes. Sarcomatoid differentiation is a morphologic change that can be seen in all subtypes that typically portends a poor prognosis. In the past, treatment options for RCC were limited to cytokine-based therapy with a high-toxicity profile and low response rate. An increased understanding of the molecular basis of RCC has led to substantial improvement in treatment options in the form of targeted therapy and immunotherapy. A significant early discovery in RCC was frequent inactivation of the Von Hippel Lindau gene in ccRCC, which ultimately led to the development of vascular endothelial growth factor and mammalian target of rapamycin inhibitors. Further genomic sequencing of ccRCC tumors has identified other common mutations including BAP-1, PBRM1, SETD2, and PIK3CA. Many recent studies have explored how these mutations can affect prognosis and response to treatment. Likewise, papillary RCC has also been studied at the molecular level, which has shown a high level of mutations in the MET gene; early clinical data suggest the utility of MET targeted therapy. Finally, regarding the rarer sarcomatoid tumors, mutations in TP53 and NF2 may be important to their development. As we continue to learn more about what drives RCC at the molecular level, treatment options for RCC patients are diversifying.