Microbiome-metabolomics analysis for biomarker identification in liver cancer among Rio Grande Valley Hispanics.

Abstract

e16268 Background: Rio Grande Valley (RGV) Hispanic population is a major hotspot for hepatocellular carcinoma (HCC) and liver diseases. HCC often develops from metabolic dysfunction-associated steatotic liver disease (MASLD), progressing through stages like simple steatosis, MASH, and cirrhosis. We explored microbiome-metabolome associations, uncovering microbe-metabolite links in RGV patients that would potentially guiding future diagnostic and therapeutic strategies. Methods: DNA extraction was performed from FFPE tissue blocks from MASLD, MASH, HCC, and cirrhosis using the QIAamp DNA FFPE Advanced Kit and assessed with Qubit and TapeStation. 16S rRNA metagenomics was performed on Illumina MiSeq and Taxonomic classification with Kraken 2. Microbial diversity and comparative analyses were performed using R packages, Welch t-tests and Bray-Curtis ordination and metabolomics using Bruker and Thermo instruments. Results: Microbiome analysis of liver tissues revealed Proteobacteria as the dominant phylum in MASLD, followed by Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria , all significantly reduced in MASH, Cirrhosis, and HCC. MASLD showed a greater abundance of Beijerinckiaceae, Moraxellaceae, Streptococcaceae, and Enterobacteriaceae . Alpha and beta-diversity analyses demonstrated distinct microbiome clustering across disease stages, with significant differences between MASLD and HCC. Genus-level differences included increased Ruminococcus, Enterobacter, Ellagibacter, and Enterococcus in MASH and higher Collinsella, Veillonella, and Prevotella in Cirrhosis. Species-level analysis identified Ruminococcus callidus, Enterobacter kobei, Staphylococcus warneri, and Kocuria rhizophila in MASH, while MASLD was enriched with Bifidobacterium thermophilum, Lacticaseibacillus rhamnosus, and Lactobacillus spp. Notably, MASH-Stage II showed increased Ralstonia pickettii, Prevotella salivae, Streptococcus mutans, and Lachnoanaerobaculum sp . compared to MASH-Stage I. Microbiome-metabolomics integration revealed correlations between microbial composition and metabolic activity, with Spearman correlation further confirming links between microbiome diversity and liver disease progression. These findings suggest a potential role for microbiome-targeted strategies in MASLD and liver disease management. Conclusions: This study is crucial for identifying the etiology of HCC and developing microbial species-based diagnostic and prognostic biomarkers. It is particularly relevant for the Hispanic population in the RGV, addressing a significant regional health disparity.