Chen, Jun

Abstract Breast cancer is the leading cause of cancer death among women worldwide. Most cases occur in those without identifiable modifiable risk factors, highlighting critical gaps in our understanding of breast cancer biology including the influence of the gut microbiome. Here we studied the gut microbiome with shallow shotgun metagenomic sequencing from preoperative stool samples in a well-characterized clinical cohort of 131 women, median age 59 years, undergoing breast-conserving surgery for benign (n=23), high-risk (n=47), or malignant (n=61) breast disease. Taxonomic profiling was performed with Sourmasth 4.2.4 with GTDBv202 as reference database; functional profiling of metagenomic data employed HUMAnN 3.6 with identified gene families mapped to MetaCyc pathways. Differences in alpha diversity in terms of species richness were observed across diagnosis groups (benign, high-risk, malignant) and was lowest for high-risk lesions (p=0.031). Decreased alpha diversity was also associated with higher body mass index (BMI) (Shannon p=0.12, Inverse Simpson p=0.025). Significant beta diversity differences across diagnosis groups also were seen (Bray-Curtis p=0.044, Jaccard p=0.013) as were differences in association with BMI (Bray-Curtis, Jaccard, both p=0.002). No significant diversity differences associated with age, mammographic breast density or menopausal status were observed. Functional pathway profiling stratified by BMI showed a correlation between increasing BMI and greater relative abundance of genes in nicotinamide adenine dinucleotide (NAD) biosynthesis, folate metabolism, and aromatic amino acid metabolism pathways (p=0.0279, 0.0667 and 0.0860, respectively) - pathways implicated in breast cancer detection, survival and prognosis. Cross-referencing our significantly (FDR <5%) differentially abundant taxonomic findings with these functional pathway data identified enrichment of several Blautia species, linked to NAD biosynthesis via tryptophan metabolism, in patients with higher BMI. We also noted enrichment of Dorea formicigenerans, a species associated with increased breast cancer risk in obese women due to its pro-inflammatory effects, in individuals with a higher BMI. Here we report significant differences in gut microbiome diversity, taxonomy and functional pathway signals in association with BMI in women with breast disease. Differentially abundant species seen with rising BMI may contribute to functional pathways that drive increased breast cancer risk and may provide an actionable target for risk reduction independent of conventional risk reduction strategies. Citation Format: Jack W. Sample, Matteo Redaelli, Stephen Johnson, Tanya L. Hoskin, Marina R. Walther-Antonio, Jun Chen, Tina J. Hieken. Obesity alters cancer-related microbial pathways in women with benign and malignant breast disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2213.

Abstract The role of maternal microbiome transmitted at birth in cancer control is poorly understood. We have developed the first germfree B6 mouse model of breast cancer to investigate the role of the maternal microbiome in controlling oncogenic/metastatic frequencies of pro-oncogenic mammary cells. In this model, a DNA barcoded, primitive normal mouse mammary epithelial cell encoding MMTV-PyMT oncogene, was transplanted in large numbers into conventional or germfree B6 mice. Next-gen sequencing analysis of the DNA barcodes in tissues enabled us to clonally track millions of cells and measure the frequency and growth dynamics of clones at the primary site and their systemic distribution in circulation and all vital organs, generating an unprecedented high-definition map of cancer progression. Our results show that in conventional B6 mice with maternal microbial transmission at-birth, a small fraction (~0.01%) of transplanted cells transform de novo and produce slow growing, late-onset benign tumors (mouse median survival of > 1 year). In contrast, in germfree B6 mice, a >10-fold higher frequency of cells transform de novo and generate early-onset, highly aggressive metastatic clones, and are frequently associated with features leading to early euthanasia or endpoint (i.e. sudden death, intracardiac metastasis, paralysis, swollen abdomen, early multiorgan aggressive metastasis) (median survival of ~4 months; p<0.005 vs conventional mice). However, postnatal intervention with healthy fecal implants reconstituted gut microbiota in germfree B6 mice and significantly restored protective effects against cancer progression and sudden death, as well as improved quality/duration of life (median survival of >1 year; p<0.005 vs germfree mice; p=ns vs conventional mice). We found maternal microbial transmission fully protected against systemic metastasis. GC-MS analysis identified significantly distinct primary tumor metabolome associated with conventional (non-metastatic) mice vs germfree (metastatic) mice. Metagenomic analysis of fecal samples from a subset of tumor bearing conventional (non-metastatic) mice vs fecal implanted (late-onset, less aggressive metastatic) germfree mice identified significant association between metastasis and altered microbial communities. These findings using novel germfree mouse model of metastasis and cellular DNA barcoding technology provide first direct evidence that diverse microbial communities transmitted at birth play a critical role in protecting the host from clonal de novo mammary cell transformation and progression to systemic disease and thereby improving quality and duration of life. Citation Format: Nagarajan Kannan, Syed Mohammed Musheer Aalam, Xiaojia Tang, Krishna Kalari, Purna Kashyap, Jun Chen, Stephen Johnson, Anguraj Sadanandam, Mark Sherman. Maternal microbiome protects host against clonal de novo transformation, early onset systemic metastasis, and sudden death [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB226.

Abstract Summary: The development of the Infinium HumanMethylation450 BeadChip enables epigenome-wide association studies at a reduced cost. One observation of the 450K data is that many CpG sites the beadchip interrogates have very large measurement errors. Including these noisy CpGs will decrease the statistical power of detecting relevant associations due to multiple testing correction. We propose to use intra-class correlation coefficient (ICC), which characterizes the relative contribution of the biological variability to the total variability, to filter CpGs when technical replicates are available. We estimate the ICC based on a linear mixed effects model by pooling all the samples instead of using the technical replicates only. An ultra-fast algorithm has been developed to address the computational complexity and CpG filtering can be completed in minutes on a desktop computer for a 450K data set of over 1000 samples. Our method is very flexible and can accommodate any replicate design. Simulations and a real data application demonstrate that our whole-sample ICC method performs better than replicate-sample ICC or variance-based method. Availability and implementation: CpGFilter is implemented in R and publicly available under CRAN via the R package ‘CpGFilter’. Contact: chen.jun2@mayo.edu or xlin@hsph.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online.