All authors supported publication of this manuscript. Competing interestsThe authors declare that they have no competing likes and dislikes. Footnotes Publisher’s Note Springer Nature remains neutral with regard to jurisdictional statements in published maps and institutional affiliations. Chunying Liu, Xuejing Lin and Bin Sun contributed equally to this work. sets used and/or analyzed during the current study are available from your related author on sensible request. Abstract Background and goal The proline rich mitotic checkpoint control element (PRCC) is involved in the splicing process of pre-mRNA. This study seeks to elucidate PRCC molecular function, regulatory mechanism and diagnostic value in hepatocellular carcinoma (HCC). Methods The cells microarray and serum samples from HCC individuals were used to investigate the medical value of PRCC. The biological function and molecular mechanism of PRCC were shown by cell biology, biochemical and animal experiments. The relationship between PRCC and intratumoral heterogeneity (ITH) was analyzed by bioinformatics. Results PRCC was highly indicated in HCC cells and related to the poor prognosis of HCC individuals, its contents were elevated in the preoperative sera of HCC individuals. PRCC exhibited high software potential as a substitute or adjuvant of alpha-fetoprotein (AFP) for medical analysis of HCC. It experienced no significant effect on the proliferation of malignancy cells, but could inhibit spheroid formation and metastasis of HCC cells in vitro and (S)-(-)-Bay-K-8644 in vivo. The high ectopic manifestation of PRCC made tumor cells insensitive to DNA damage, and enhanced the heterogeneity of HCC cells by inhibiting the JNK/ATM/ATR/ATF2 axis. The HCC individuals with high PRCC manifestation experienced high ITH, which corresponded to a short overall survival in individuals. Conclusions PRCC offers high software potential as a substitute or adjuvant of AFP for medical analysis of HCC. The high ectopic manifestation of PRCC not only caused HCC cells to resist to cell death induced by DNA damage, but also endowed malignancy cells with several DNA mutations to become increasingly heterogeneous, finally leading to a poor prognosis in HCC individuals. These data suggested PRCC could be a encouraging therapeutic target in HCC individuals. Supplementary Information The online version consists of supplementary material available at 10.1186/s13578-021-00699-x. overexpression vector. The short hairpin RNA 1 (shRNA1) and shRNA2 sequences were designed and constructed into pLKO.1 plasmid (Addgene, Plasmid #10878) to generate the knockdown vectors. The shRNA1 and shRNA2 sequences were as follows: 5-ccgggctggtgcttattatcaggatctcgagatcctgataataagcaccagctttttg-3 (shRNA1); 5-ccggacaccagatcacatatcttatctcgagataagatatgt gatctggtgttttttg-3 (shRNA2). The overexpression and knockdown vectors were packaged into lentiviruses KNTC2 antibody which were used to infect the prospective cells. The cell sublines with overexpression or knockdown of were confirmed by Western Blot. Quantitative reverse transcription PCR (RT-qPCR) Total RNA was extracted with Trizol reagent (Invitrogen, USA), and then the transcriptional levels of genes were tested by RT-qPCR. The primers involved were shown in Additional file 1: Table S1. Animal experiment Animal experiments were authorized by the Committee on Ethics of Medicine, Navy Armed service Medical University or college. All animals received humane care according to the criteria defined in the Guidebook for the Care and Use of Laboratory Animals. Eighteen purebred 6-weeks-old Balb/c male nude mice were divided into three organizations: blank control group (Hep3B), bad control group (Hep3B-EGFP) and PRCC overexpression group (Hep3B-PRCC OE). Each group contained 6 mice, and the related cell sublines were injected into the tail vein (8??105 cells/150?l per mouse). (S)-(-)-Bay-K-8644 Thirty days later, mice were sacrificed painlessly, and dissected to observe the tumor formation in lungs, livers and kidneys. HE staining was performed. Spheroid assay and immunofluorescence (IF) One thousand cells per 150?l (diluted in DMEM) were mixed with 150?l Matrigel and spread evenly inside a 24-well plate. After cultured for one week, the cell spheres appeared. The cell spheres were collected and the immunofluorescence process was carried out. The antibodies used were shown in Additional file 1: Table S2. Inhibition of cell proliferation and cell cycle After incubated for 24?h in 96-well plates, cells were treated with ultraviolet (UV) irradiation having a dose of 5?J/m2 (S)-(-)-Bay-K-8644 [Dose (mJ/cm2) = Exposure time (s)??Output intensity (mW/cm2)] and cultured for another 24?h, or cells were treated with 30?M Cisplatin (DDP) for 24?h. Then CCK8 assay was carried out, and the inhibition rate was determined. After cultured for 24?h in petri dishes, cells were treated with UV irradiation having a dose of 5?J/m2 and cultured for another 24?h, or cells were treated with 30?M DDP for 24?h. The cells were collected and the circulation cytometry was utilized for cell cycle detection. Western blot The cells were collected and lysed with RIPA lysis buffer (1% PMSF, 1% phosphatase inhibitor and 1% protease inhibitor were added). The Western blot process was carried out as typical. The antibodies involved were shown in Additional file 1: Table S2. Analysis of intratumoral heterogeneity (ITH) The solitary nucleotide variance (SNV) files based on whole-exome sequencing (WES) of 365 individuals with HCC were downloaded from your Tumor Genome Atlas (TCGA)liver and intrahepatic bile ducts (LIHC) project (S)-(-)-Bay-K-8644 of the website (https://portal.gdc.malignancy.gov/). Mutant-allele tumor heterogeneity.