Phenylalanine Reprograms TLS Maturation and Plasma cell differentiation in MASH-HCC [scRNA-seq]

Metabolic dysfunction–associated steatohepatitis (MASH) is a rapidly growing cause of hepatocellular carcinoma (HCC) and is associated with poor clinical outcomes and limited responsiveness to immune checkpoint inhibitors. Emerging evidence suggests that immune dysregulation within the tumor microenvironment contributes to disease progression; however, the transcriptional programs distinguishing MASH-associated HCC from non-MASH HCC remain incompletely characterized. To address this gap, we performed bulk RNA sequencing on total RNA isolated from MASH and non-MASH tumor tissues. This dataset was generated to enable comparative transcriptomic analysis of tumor-intrinsic and immune-related pathways associated with MASH-driven hepatocarcinogenesis, with particular relevance to immune organization, metabolic stress responses, and tumor–immune interactions.The resulting RNA-seq data provide a resource for investigating alterations in immune cell–associated gene signatures, metabolic pathways, and microenvironmental features that may underlie immune dysfunction in MASH-HCC. Overall design: C3H mice were fed a 60% kcal high-fat diet (HFD; Research Diets, Inc.) for 8 weeks. To induce nonalcoholic steatohepatitis (NASH), mice were then switched to a modified methionine- and choline-deficient (MCD) diet formulated to contain 60% kcal from fat (Research Diets, Inc.). Age- and sex-matched control mice were maintained on a non-NASH control diet. The establishment of the NASH phenotype was confirmed after dietary intervention using standard histological and metabolic assessments prior to tumor inoculation. Following confirmation of NASH, mice in both NASH and control groups were subcutaneously inoculated with the HCA-1 murine hepatocellular carcinoma cell line. Tumor growth was monitored and measured for 4 weeks. At the experimental endpoint, tumors were harvested, snap-frozen in liquid nitrogen, and stored at -80 °C until processing. For RNA extraction, frozen tumor tissues were pulverized using a mortar and pestle under liquid nitrogen. TRIzol reagent was added directly to the homogenized tissue, and total RNA was extracted according to the manufacturer's protocol. RNA purity was assessed by spectrophotometry (260/280 ratio), and high-quality RNA samples were submitted to Novogene for bulk RNA sequencing.