Machine learning and single cell RNA sequencing analysis identifies regeneration-related hepatocytes and highlights a Birc5-related model for identifying cell proliferative ability

Abstract

Background Partial hepatectomy (PHx) has been shown to induce rapid regeneration of adult liver under emergency conditions. Therefore, an in-depth investigation of the underlying mechanisms that govern liver regeneration following PHx is crucial for a comprehensive understanding of this process. Method We analyzed scRNA-seq data from liver samples of normal and PHx-48-hour mice and identified a population of highly proliferative hepatocytes 48 hours after hepatectomy. Seven machine learning algorithms were utilized to screen and validate a gene signature that accurately identifies and predicts this population. We also used co-immunostaining of zonal markers with BIRC5 to investigate regional characteristics of hepatocytes post-PHx. Results Single cell sequencing results revealed a population of regeneration-related hepatocytes. Of note, transcription factor analysis emphasized the importance of Hmgb1 transcription factor in liver regeneration. HdWGCNA and machine learning algorithm screened and obtained the key signature characterizing this population, including a total of 17 genes, most of which have been confirmed to be related to liver regeneration, and the function enrichment analysis indicated their high correlation with cell cycle pathway. Furthermore, we found that the spatial characteristics of hepatocytes gradually weakened during regeneration and immunostaining further revealed that those hepatocytes with active proliferative ability primarily initiate in the midlobular zone and then repopulated peripheral region. It is note-worthy that we inferred that Hmgb1 might be vital in the regeneration-related hepatocytes of PHx_48h group. Parallelly, Birc5 might be closely related to the regulation of liver regeneration, and positively correlated with Hmgb1 while negatively correlated with portal vein and central vein characteristics. Conclusions Our study has identified a distinct population of hepatocytes that are closely associated with liver regeneration. Through machine learning algorithms, we have identified a set of 17 genes that are highly indicative of the regenerative capacity of hepatocytes. This gene signature has enabled us to assess the proliferation ability of in vitro cultured hepatocytes using sequencing data alone. Furthermore, our findings suggest that Birc5 may play a crucial role in regulating the proliferative potential of hepatocytes.