This multi-omics study delves into the expression patterns of PIWIL genes and their correlation with hepatocellular carcinoma (HCC) progression, utilizing whole transcriptome sequencing, bioinformatics, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) in mice. We identified differential expression levels of PIWIL genes between HCC and control tissues and analyzed their roles within the competing endogenous RNA (ceRNA) network related to regulatory non-coding RNA-mediated gene silencing (RNGS). Our findings showed that
Piwil1
and
Piwil4
were overexpressed while
Piwil2
is underexpressed. As ceRNAs, specific lncRNAs, including
Pvt1
,
Gas5
, and
BGIGI10090_38749
, might sponge up miR-351-5p and miR-31-5p, promoting
Piwil1
and
Piwil4
expression, while miR-133b-3p, lacking ceRNA sponge absorption, continues to inhibit
Piwil2
. Through their interactions with PPI proteins encoded by RNGS genes, especially
Dhx9
,
Drosha
,
Mov10
, and
Tdrd1
, PIWI family members might play a multifaceted role in regulating gene expression and metabolic processes, thereby involving the development and progression of HCC. These interactions within the PPI network could influence the stability and activity of PIWIL proteins and contribute to the overall regulation of gene expression and HCC progression. In the RNGS, a diverse array of miRNAs, genes, lncRNAs, circRNAs, and pseudogenes have been observed, which are suggested to intricately interplay, potentially weaving a complex ceRNA regulatory network. Abnormally expressed miRNA-targeted genes in RNGS are associated with key biological processes, such as lipid metabolism and immune responses, crucial for tumor cell survival, and processes supporting tumor growth and invasion, like translation and cytoskeleton organization. This regulation is reflected in distinct KEGG pathways for downregulated and upregulated targets, highlighting the dualistic role of PIWIL genes in modulating HCC progression. The study concludes that PIWI family members have a correlation with HCC progression and play divergent roles in the pathogenesis, with overexpression of the
Piwil1
and
Piwil4
potentially promoting HCC progression and underexpression of
Piwil2
likely suppressing tumor development. The ceRNA mechanism and PPI network are crucial in regulating the expression and function of PIWIL genes, respectively. The intricate ceRNA network potentially regulates the expression of miRNA-targeted genes in RNGS, which might be crucial for tumor survival and promotion, with impacts on immune responses and cell growth based on enriching results of dysregulated miRNA-targeted genes in HCC. By shedding light on the molecular int...